Yes, fluff descriptions are part of the rules. How do I know? Look, they're written in the rulebook.
The question becomes, how much of what is in the rulebook is it permissible for you to override or discard? The answer is based on context.
In your home game - up to and including all of it! Of course, that applies to the advice, the fluff, and the rules as well. The books explicitly tell you to change or disregard things as it suits your game. It is becoming a common practice to re-skin; there's extensive discussion of it as a practice in Pathfinder podcasts for example (3.5 Private Sanctuary/Know Direction, Pathfinder Chronicles; the Gamer's Guide to Pathfinder had an entire episode on the practice). It's not really touched upon in the crunch section of rulebooks as it's a "meta" practice (like do you fudge rolls or not...). But, in the advice type sections, you're in luck! (Here's where owning and reading the actual books is better than just using the free SRD.)
The Pathfinder GMG specifically mentions reskinning for GMs -
"Another trick is to “re-skin” one adventure with a different flavor, such as taking a fire-themed temple and
changing all encounters, spells, and monsters from fire
to cold as the players go through it."
"That’s particularly true
in an emergency situation where you’re likely going to “reskin”
the monsters anyway. That armored knight? You can
just describe him as a hill giant and your players will never
know. Then you can make him into a dire wolf, or a swarm
of killer bees, and still your players may never know. Sure,
you’ll know that the damage dice should have been different,
the skills were completely irrelevant, the Armor Class was
wrong, and the special abilities were made up on the spot,
but you’re the only one who sees the stat block. Everyone else
is just rolling dice and having fun."
So reskinning is explicitly declared as a legit, good tactic for GMs for monsters and adventures. Since you're the GM, you can also allow PCs to reskin as you see fit. In my games, I see zero problem with reskinning - if there's no rules impact, it's all good. So yes, you can be a freebooter rules-wise but depict yourself in any number of different ways.
The Animal Archive backs this approach, saying:
As a player, you may desire a special familiar—either real, unique to your campaign world, or wholly imagined—that hasn't yet been presented with specific stats. With your Gamemaster's approval, however, it's easy to “re-skin” an existing familiar stat block to create the exact familiar you want.
In a Pathfinder Society game - none of it can be reskinned. The PFS FAQ specifically disallowed reskinning of fluff for animals and items:
Can I re-skin or re-flavor an animal companion or item?
You may choose a specific type of animal companion from any of the base forms listed on pages 53–54 of the Pathfinder RPG Core Rulebook or a legal Additional Resource but may not use stats for one base form with the flavor of another type of animal. Thus,
a small cat could be a cheetah or leopard, as suggested, as well as a lynx, bobcat, puma, or other similar animal; it could not, however, be "re-skinned" to be a giant
hairless swamp rat or a differently-statted wolf. If a GM feels that a re-skinning is inappropriate or could have mechanical implications in the specific adventure being played, he may require that the creature simply be considered its generic base form for the duration of the adventure. A player may not re-skin items to be something for whic
h there are no specific rules, and any item a character uses for which there are no stats is considered an improvised weapon (see page 144 of the Pathfinder RPG Core Rulebook).
And in general reskinning is disallowed for other things as well - if there's a friendly individual GM that lets you, that's one thing, but all the campaign rulings have been against it. PFS exists to provide a standardized generic Pathfinder experience for the masses and this they don't allow reskinning.
See also To what extent is reskinning acceptable? for 4e and What are the commonly accepted definitions of reskinning and refluffing? for concept discussion.