The way just about everyone plays this is that if a bonus feat names a specific feat, you get it and can use it regardless of requirements. If a bonus feat allows you to get a feat of your choice (off of a particular list, or just any feat at all), you have to qualify both to select it and to use it. The obvious exception in both cases is when whatever is giving you the bonus feat explicitly says otherwise.
But the rules don’t just come out and say that. And this consensus doesn’t come, for the most part, from a careful reading of any rules—this is just a common ruling based on what most people “expect” to be the rules. So the question becomes, do the rules actually match people’s expectations?
Rules as written
There are, effectively, three possibilities here:
The rules match our expectations
The rules fail to allow us to use even specific, named bonus feats, leading to dead feats in cases like the fleshcrafter.
When choosing a feat off of a list, the rules allow us to choose and use feats we don’t qualify for, which seems to badly imbalance classes like the fighter.
In other words, we really do want the rules to say 1, and really don’t want the rules to say 2 or 3. We’d actually really like for the rules to be clear about this.
Unfortunately, they are not, at least for cases like the fleshcrafter where the specific rules of the thing giving you the bonus feat don’t mention prerequisites. In such cases, the only rule about bonus feats’ prerequisites that we could maybe look to is,
Sometimes a creature has one or more bonus feats, marked with a superscript B (B). Creatures often do not have the prerequisites for a bonus feat. If this is so, the creature can still use the feat.
(Monster Manual, Reading the Entries, Statistics Block, Feats, pg. 7)
This statement is in a section explicitly devoted to explaining how how to read the Feats line of monsters’ statistics blocks. Does it apply to anything else? That is, is the rule that creatures can use bonus feats even if they don’t have the requirements specific to bonus feats indicated by B in a monster stat block, or does it apply to anything called a “bonus feat”?
The problem comes down to, basically, what context, if any, is supposed to matter here, and how much? The organization of the rules here, within the Monster Manual, under the “Reading the Entries” header, etc., means we expect to only find rules about that here. Furthermore, the first sentence, “Sometimes a creature has one or more bonus feats, marked with a superscript B (B),” is specifically about that topic; the B isn’t used elsewhere.
But consider the second and third sentences, “Creatures often do not have the prerequisites for a bonus feat. If this is so, the creature can still use the feat,” taken out of context. These are fairly absolute statements about “creatures” and “bonus feats,” whether that creature is in the Monster Manual or not, whether that bonus feat is due to a B in its monster entry or not. Nothing in these sentences limits the claims made to the topic of the paragraph and section—should they be read as “inheriting” those from their surrounding context, or are these supposed to simply be true statements, for all creatures and bonus feats?
Either way, there is an error in the rules here: either these two sentences were meant to only apply to monsters, should have been clearly limited to bonus feats marked with B in monster statblocks, or else it was meant to be general, and so should have been found in the general rules. As written, we can’t really tell, because they didn’t do either of those things when they really needed to do one or the other.
We can try to inject some more context into this ambiguity, though. Among classes, the monk is the ur-example of bonus feats ignoring prerequisites.1 Here’s how that’s worded:
A monk need not have any of the prerequisites normally required for these feats to select them.
(Player’s Handbook pg. 41)
As you quote, and quite correctly emphasize, “Your character must have the indicated [prerequisite] in order to select or use that feat.” The monk class waives this rule for selecting the feat—but not for using it. If the monk still needed the prerequisite to use the feat, they wouldn’t be able to, particularly in the case of Stunning Fist (requires BAB +8 when a 1st-level monk has +0). Meanwhile, the Monster Manual rule says you can use a bonus feat without prerequisites—but says nothing about selecting (monsters don’t select bonus feats they are just printed with bonus feats). Together, they combine to allow the monk to do both.
Notably, this means that the Monster Manual rule doesn’t break the fighter or rogue—since both classes offer a bonus feat of your choice, you must select one in order to get it, and neither class says you can select a feat you don’t qualify for. Thus, nothing says that, and you can’t. So fighters and rogues are still limited to bonus feats they actually qualify for.
In the case of the fleshcrafter, you also don’t have to worry about selecting, since the class feature just says you get the feat, no selection necessary. You don’t have any more choice about it than monsters in the Monster Manual do. But the Monster Manual rule can still allow you to use that feat.
If it applies. Which is still ambiguous. But through a convoluted logic, if we accept the Monster Manual rule, then the near-universal consensus also matches the actual rules as written. Whether or not that “if” is valid, it seems pretty strong that this is the right way to rule things at your table. There doesn’t seem to be any good reason to break the monk or the fleshcrafter ruling otherwise.
- The core base classes that get any bonus feats at all are the fighter, monk, ranger, and rogue. The monk is the only one to explicitly waive prerequisites in general, and one of its major class features is the ability to get Stunning Fist at 1st when it is otherwise inaccessible until 8th level at the earliest. By contrast, the fighter and rogue both allow you to choose a feat out of a wide array of options, and don’t suggest you can ignore any requirements in the process. Meanwhile, the ranger talks about requirements at length for its combat styles, explicitly noting you can ignore the usual prerequisites but you have new prerequisites, and anyway the ranger emphasizes that you are “treated as having the [chosen] feat,” rather than actually having the feat per se. The ranger’s Track and Endurance bonus feats are irrelevant here since they don’t have prerequisites to begin with. For more on the “virtual feats” from a ranger’s combat styles, see Masters of the Wild, pg. 20.