That section from the CRB is explaining how spells usually work. It's not providing prescriptive rules from the game, it's just explaining to you what usually happens, because usually multiple copies of the same buff spell don't really do anything since their same-typed bonuses don't stack, or because they give you an option for their duration and multiple sources of access to a single option isn't really helpful, or because they grant immunity to some source of danger, and additional immunities to that single thing are rarely helpful.
So, generally, you can have multiple active instances of any spell, the additional instances just don't do much.
That said, the specific spells in question do limit via their text their interactions with one another. You can certainly have Protection From Energy (fire) and Resist Energy (Acid) up at the same time, but if you instead ward against a single energy type, the reservoir provided by Protection from Energy is not protected by the Resist Energy effect.
Draconic Reservoir specifies that it does not stack with Protection from Energy, but technically that doesn't prevent you from using it alongside that spell. When two beneficial effects don't stack you have to take the largest bonus, so doing so gets weird since what the 'largest bonus' is supposed to be in this context is unclear. In my experience, people tend to have the pool with the most points left in it at the time apply to any given attack.
Stacking any of these spells with itself is in no way proscribed, and generally significantly increases the defensive effects:
Protection from Energy and Draconic Reservoir can each be self-combined either to provided separate pools for multiple energy types or to create what is effectively a larger single pool for one energy type.
Resist Energy Energy resistance from multiple sources stacked in 3.5, except that energy resistance not from spells couldn't stack with energy resistance from spells. Pathfinder kept this rule, almost verbatim
James Jacobs, creative director for Pathfinder, however, has said that "Energy Resistance does not stack". No explanation for this counter-textual ruling has thus far been provided, except that being a tiefling infernal bloodline sorcerer is supposed to "suck for [electrical resistance]", at least until level 20.