Uhhh.
I'm going to be a bit out of the box here and recommend you consider using
Arch Linux ARM instead. Obviously as a member of the Arch Linux project and maintainer of the calibre package I'm a bit biased, but Arch really is much easier with regard to this sort of dependency kerfuffle. And we provide always-up-to-date packages more or less immediately.
As long as you have someone pay attention to what happens when you update the system, it should be more or less painless. I've found Arch to be extremely stable actually.
From quickly glancing at your Github, it looks like you deploy these rpis using ansible anyway, so it should be fairly simple to test an update then roll the deployment out to all the various installations.