I am not certain I quite follow you. Do you mean to say that calling in a favor from the Unseen Court is not actually any more costly than doing so with Flint or Risur?
Maybe asking a fey for a favor has a more random component to how exactly they'll help you. So, for example, if you'd want a nymph to lure a Kell guild member from the Nettles to Cloudwood to interrogate him, maybe she'll find interest in his girlfriend or squad as well and you have do deal with more than one charmed captive. Or the nixie you'd like to get an invisibility potion from wants you to dance the hokey-pokey in front of Lee's Barbershop (because she likes that old man and wants to cheer him up).
A good DM won't use the fey prestige requests as secret means to punish his players, but as means to put some life into the fey society and maybe hook you up on some sidequest.
For Prestige in general: I don't know how the other groups handle this mechanic, but we usually use it only as rule of thumb for what's appropriate to ask for. For example, we're in adventure 5 now (no spoilers!) and desperately need more officers in Flint. So we do some calculation, describe our case and circumstance and then get an answer on how soon we can expect help.