The GM is responsible for balancing character's wealth
Basically, the wealth-by-level table and rules are simply guidelines for GM (and by extension, adventure writers) to have an idea of what kind of treasure they can include as rewards for their encounters. The exact wealth of the characters is not really set in stone, and proof of that, is that the value can easily range between 50% and 200% of the indicated value on that table.
Table: Character Wealth by Level lists the amount of treasure each PC is expected to have at a specific level. Note that this table assumes a standard fantasy game. Low-fantasy games might award only half this value, while high-fantasy games might double the value. It is assumed that some of this treasure is consumed in the course of an adventure (such as potions and scrolls), and that some of the less useful items are sold for half value so more useful gear can be purchased.
While item-creation feats can easily change that value to around 25% to 50% more accumulated wealth in a given level.
However, game balance for the default campaign experience expects you and all other PCs to be close to the listed wealth values, so the GM shouldn’t just let you craft double the normal amount of gear. As a guideline, allowing a crafting PC to exceed the Character Wealth by Level guidelines by about 25% is fair, or even up to 50% if the PC has multiple crafting feats.
Another example of this are the Adventure Paths (paizo's monthly published adventures), some of them break wealth-by-level by enormous amounts, like when players are given artifacts, or the control of certain high-valued resource (like a kingdom, or a walking-hut), or are simply given way more wealth than they should because the adventure will be tougher later on on treasures.
Abilities that change wealth by level
Yes, there are dozens of abilities that will grant an economic advantage in the game, however, none of those are big advantages, they are always minor bonuses, like 10% discounts, sell for 10% more, or replacing the need to find an item in your local market.
If you look at them closely, they are not direct increases in wealth by level, but simply small adjusments that are well within the guidelines i mentioned before (50% to 200%). Sometimes the gain isn't even worth the investment like spending a feat for 10% sell value is nowhere worth the value of a feat, since all sold gear is already 50% of the wealth-by-level worth of that item.
When you sell gear, you are diminishing the wealth by level of the group in favor of customization, so you can buy something better suited for your characters instead of using whatever treasure you got. The wealth generated by magic items is ofset by this, since you must sell treasure to obtain the materials to craft. But the gain is still much bigger from magic item creation feats than most feats that grant discounts or overcharges, since you are allowing the group to customize whatever treasure they got.
For example: Your character is a wizard, but the group got a 2,000 worth magic sword, since you have the abilities to craft wondrous items, the party decides to sell that sword and use the resources to craft magical goods. They sell that 2,000 sword for 1,000 gp (their treasure got cut in half). And now the wizard spends a few days crafting two cloaks of resistance. These cloaks cost 1,000 gp to buy, and thus 500 gp to craft. He decides to craft two of them with the money they got, for a total of 1,000 gp in materials and two days of work. The party's gain was two magical cloaks worth 1,000 gp each, or 2,000 gp (the same treasure value of the magical sword).
Now, let's say the party's rogue has the feat to sell items for 60% instead of 50% of the market price. That 2,000 sword now sells for 1,200 gp instead of 1,000 gp. The party gained 200 gp on the treasure, or 10% more treasure. Instead of 100%, they now have 110% of the expected treasure at their level. Which is acceptable by the rules.
The kingdom building rules are a complete exception to wealth by level. Kingdoms are a high valuable resource that should only be available in a game that is built for those rules (it's an optional system afterall). You cannot go and tell your GM "we are building a kingdom" and expect an "Yes." all the time, specially if the GM isn't familiar with these rules, and the group as a whole willing to follow that gameplay style.
That said, the wealth of the group is much higher when they own a kingdom than when they dont, you cannot expect to balance those unless the GM is rigit about the population's response against tyrants that uses their taxes for personal profit.
Another exception is the spell Blood Money. Unlike most, this spell trades ability damage for real money. This, over the levels, can increase the wealth of the character. But this spell is only available on an adventure that is not open content, or part of the PRD, and is obtained from a spellbook of a mage from an ancient (dead) civilization (at nearly the end of the campaign), not on your local scroll-shop.
Personally, i don't think the gain even justifies worrying about it, the spell has limited uses, as you can only use it with spells that are cast on the same round as the spell.
The point is that how much wealth the group has can be controlled by the GM.
By adjusting encounters to increase wealth or to decrease wealth
Encounters with lots of creatures (CR lower than the average party level) will probably spend lots of resources, be in the form of renewable resources (spells, daily abilities) or expendable resources (potions, wands, scrolls).
While encounters with a few strong creatures (CR higher than the average party level) can result in character death, or some form of debilitation that you must spend money to remove, such as curses, negative levels, or resurrections.
The GM is supposed to follow the guidelines presented on the Gamemastering chapter of the core rulebook (page 399-401 on sixth printing):
Placing Treasure
As PCs gain levels, the amount of treasure they carry and use increases as well. The game assumes that all PCs of equivalent level have roughly equal amounts of treasure and magic items. Since the primary income for a PC derives from treasure and loot gained from adventuring, it’s important to moderate the wealth and hoards you place in your adventures. To aid in placing treasure, the amount of treasure and magic items the PCs receive for their adventures is tied to the Challenge Rating of the encounters they face—the higher an encounter’s CR, the more treasure it can award.
Table: Character Wealth by Level lists the amount of treasure each PC is expected to have at a specific level. Note that this table assumes a standard fantasy game. Low-fantasy games might award only half this value, while high-fantasy games might double the value. It is assumed that some of this treasure is consumed in the course of an adventure (such as potions and scrolls), and that some of the less useful items are sold for half value so more useful gear can be purchased.
(...)
Table: Treasure Values per Encounter lists the amount of treasure each encounter should award based on the average level of the PCs and the speed of the campaign’s XP progression (slow, medium, or fast). Easy encounters should award treasure one level lower than the PCs’ average level. Challenging, hard, and epic encounters should award treasure one, two, or three levels higher than the PCs’ average level, respectively. If you are running a low-fantasy game, cut these values in half. If you are running a high-fantasy game, double these values.
Encounters against NPCs typically award three times the treasure a monster-based encounter awards, due to NPC gear. To compensate, make sure the PCs face off against a pair of additional encounters that award little in the way of treasure. Animals, plants, constructs, mindless undead, oozes, and traps are great “low treasure” encounters. Alternatively, if the PCs face a number of creatures with little or no treasure, they should have the opportunity to acquire a number of significantly more valuable objects sometime in the near future to make up for the imbalance. As a general rule, PCs should not own any magic item worth more than half their total character wealth, so make sure to check before awarding expensive magic items.
As we can see, the wealth of the group is completely in the hands of the GM.
He has the power to:
- Pick creatures without treasure (animals, oozes, plants) and make a whole dungeons with them, awaring very little treasure.
- Pick many encounters with treasures (humanoids, dragons), which should award more treasure than normal.
- Add traps and enviromental hazards to the adventure, which by themselves give no monetary reward at all.
- Increase their treasure by simply offering rewards for quests and things their characters would already have done even without a reward ("We need someone to kill that black dragon that has been plaguing our village, and will offer a 1,000 gp reward for anyone brave enough that does so"), which simply injects wealth into the group that comes from other sources.
