Soulbinds and such would have to work differently, you wouldnt want to mix and match Necrolord abilities with Kyrian Soulbinds or something. And the Mission table would need to work somewhat differently, but other than that I think it would work. It would certainly give players an incentive to use all the extra anima they gather.
Point is to make a version of the system that lets you have an easier choice between covenants without removing most of hte meaningful choice, and also to give a better incentive on where to dump the frankly irresponsible amounts of Anima the game dumps on you, and likely will continue to give more of as the expansion goes.