Yep, even though you mention using Linux in your doc, here's Calibre: https://calibre-ebook.com/. On the downloads page you'll see that it supports Linux, Mac, and Windows, a true cross-platform open source app.

On formats and devices: get the device that you prefer the overall physical characteristics and don't be driven primarily by the file format. If you find a device where you are happy with the storage, the screen, the ergonomics, and the user experience with the software, get that device. Almost everything out there will support .Mobi, .Epub, or both, and you can easily convert every book you have to both formats.

A few I'd look at would be the latest Kindle PW4 and Oasis 2, and the Kobo Forma, H20, and Clara. You might also consider testing a scenario that a few of us have at times, and that is try to get by with just a combination of your phone, and a small Android tablet in the 7" to 8" range. This will run into some of the pros/cons you mention in your doc, but, ereaders have cons too. Everything is a trade-off.