Well, one thing to consider about something like how uber-potent a FBC would be is that, in correlation to this factor, it should be exceedingly hard to get a hold of. It should be less of a 'I can buy it cause I have the dosh', and more of a 'how many hoops can you jump through to get it' sorta deal. Heck, you'd thusly do the same with each thing you could augment; make it less of a shopping list, more of a 'reward' for pursuing a certain course of action.
Heck, even The Witcher 2 did that; you'd be able to craft certain armors or the like only if you pursued a particular course of action that netted you the alchemical resources to make them - if you chose to roleplay Geralt in a fashion that he wouldn't kill a certain creature, or wouldn't betray a certain person, then you wouldn't get those items, but instead you'd get somethin' else in corresponding fashion. Consider the strongest weapons you can get by the final chapter; those are completely optional, and in some cases the result of pursuing a series of subquests across multiple chapters prior.
There's no reason we can't do that here as well, with FBC's being the end-reward after a series of decisions made, paths taken and such; its quality also relevant in such a manner too.
I'm reminded of Fallout 2, in fact, where you can get a brain implant, but you need a skilled enough surgeon to plant it in you. You get, like, three or four options, each with varying skill levels, and each with varying moral choices you must make in order to convince them to help you. The very BEST surgeon is an amoral bastard who is part of Vault City, and therefore has access to the best machinery and tools, the best education, but at the same time is utterly corrupt and wants you to do his dirty work for him.
Incidentally, you can then try to blackmail this guy.. with hilarious results:
So yeah, I see no issue with there being 'compromises' that you'd need to make, morally, or on a personal level for your character, or whatever that may be, in the pursuit of power. Or maybe you're just an amoral monster, and shedding your humanity thus comes naturally to you.