In my set-up it's the other way around. Although in response to your comment without the systems I have in place, yes you're right.
I've got a breeder alveary, so in that i have five mutator blocks with ender eyes in each, and then six frame holders with chocolate frames in each. This means that any bee I put in there has a 100% chance to mutate and 1 life cycle.
I started off with a blaze spawner, and an enderman spawner, both are fairly easy to make, just time intensive on the enderman one. So thus I have a renewable source of eyes of ender. Considering you don't automate a breeding alveary, then I think mutator blocks are definitely the way to go once you've got the infrastructure.
You are correct in saying that they're less efficient in terms of without automated systems. But you can make automated systems for the mutator block resources, and cannot for soul sand (That I have found). So once your base is up to the stage of "Automate all the things~" then mutators are the way to go.
So, soul frames to start off with, moving onto mutators afterwards.