Having two protagonists doesn't innately make more work, it is having the sheer number of of other NPCs and permutations of choice which creates the work.I think the main issue is that Eva is essentially creating 2 visual novel games at once and trying to combine both of them. It is an incredibly ambitious goal but it means that the sheer amount of choices/routes will take a super long time to write.
Of course if you have two protagonists (unless they are closely related) it won't feel authentic if they all know the same handful of characters, and the game will feel stifling if you don't give them many choices. I've played visual novels which while have choice they are essentially just kinetic because the choice literally have no ramifications, fortunately Eva hasn't gone down this route.