Exactly - interoperability is key, and is intentionally removed from many software platforms once they become big enough. Cory Doctorow writes about this here.
Companies have a funny relationship with interop. When companies are small and trying to build up their customer-base, they love interop, love the idea of selling ink for someone else’s printer or a way to read your waiting messages on someone else’s social media giant. Facebook once had a whole suite of interoperability tools to make it easy to plug Facebook into other services, but it has whittled these away over the years and today it routinely threatens and even sues rivals that try to interoperate with it.
A trend that I actually like is more software supporting using a user’s own iCloud or Google Drive as a data store rather than using the company’s own servers. The step that needs to take place is a way to use many storage providers simultaneously (including home server) with syncing behavior abstracted away. The software would essentially be a database cluster with a variety of heterogeneous nodes supported. A library that abstracts this multi-host pattern for use in both Android and iOS apps would go a long way. There is still the problem of the controller orchestrating uploads and syncs, though, which for most users would be their phone.
Upspin is new to me but looks like it’s right up this alley. Making the whole thing work for non-technical users will be one of the hard parts I imagine.
Edit: I also just saw, there is now Veilid.
It’s not an E-reader but I use a Google Nexus 7 tablet from 2013 with LineageOS and a matte screen protector. This works with Moon+, is great for PDFs and epubs, costs about 20 bucks, and syncing and loading books is very easy since it’s Android. Not what you asked for but might be a good second option if you can’t find an E-Ink reader that does what you need.