I'm trying to think of how Fate Points were used in my 40k games, and about 90% of times they're used as rerolls. The only times they weren't were when someone had Faith Powers (but only BoM ones, really, and the basic Pure Faith, as the rest of the IH stuff just never seemed worth it) and a few times when the Tzeentchian Psyker in BC used the "add d5 DoS" option when screwing with people's minds.
Maybe if the "automatically succeed" abilities were usable in lieu of a reroll they'd see more use, i.e. the sage rolls Forbidden Lore: Daemons, fails, and instead rerolling, spends FP to automatically succeed with a number of DoS determined by the ability. That'd make those abilities pretty much a straight upgrade to rerolling in specific situations, and thus quite worth it.