[NullCascade]

My suggestion is to handle it as follows:

Monster "races" (the ones defined in .user files) should not have the feats gained from monster/class hit dice (but should have the feats marked with a B -- bonus feats as part of their type) bootstrapped.

However, it would be rather nice if we went through and made .stock files out of our .user files as well. The pre-made monsters in these .stock files would let us quickly pick the default monster configs that show up when browsing the encounter builder.

This would let DMs both build custom versions of monsters when they wish to, as well as simply place the default P&P options using the built-in encounter tools. Best of both worlds, but certainly a bit of extra work for the community to get these resources made.

Example:
"3.5 - Monster Manual 1.user" -- Contains the core race, that any DM can build up as normal and customize to their heart's content.
"3.5 - Monster Manual 1.stock" -- Contains creatures that use the data from the .user file, with the feats from the related book already pre-chosen. These can be imported into a portfolio using the encounter builder, nice and searchable.