It does lack a few features though, as they rely on proprietary software/libraries. Android Auto for instace, as well as ANT+ for connecting sensors. At least for those features you need the Google Play version.
You need to be unplugged for 12 consecutive months for Proton to delete your account because of inactivity though, which seems fair for free tier accounts. A simple login is enough to prevent this, you do not need to send an email or whatever, simply log in once a year. You also get reminders sent to your recovery email before this happens. Data storage for inactive free tier accounts isn't free for Proton.
I believe you're right. However, if memory serves, the ads did change occasionally, meaning the screen had to refresh, leading to increased battery usage.
I just sent them a message asking them to disable the ads on the kindle I had recently purchased, and they did so for free, no root needed. That was a few years ago though, so I doubt they do that anymore...
I find that Neo covers most of my needs. Although there is one thing in particular that I miss: swiping actions on seperate icons to launch another app/action. I haven't used Nova in a while, but it had nicer previews inside the options, and I find that Neo has a few minor bugs that annoy me at times. But Neo has the things that are most important to me: multiple pages, tabs or folders in the app drawer, icon pack support, search and gestures (not on each icon, as noted earlier). I also miss the ability to place icons between the defined grid as in Nova.
I use KOReader both on Linux and Android, and I love it! I used Calibre's own reader for epub files earlier, but have since used a bit of time getting to know KOReader and its features better, and it suits my needs very well.
I stopped using Nova Launcher when it was aquired by an analytics company, since launchers usually have access to a lot of permissions, and I don't trust a company dealing in analytics to operate in good faith with that access. I have used Lawnchair 2 and recently switched over to Neo Launcher.