I"m not entirely sure on the pdf / epub use case, is that for RSS contents, or RSS referred contents? If it’s referred contents then perhaps use something like Omnivore or a script/plugin.
I suspect you might be mixing something that’s better done as two different apps into one. Omnivore and similar tools you would probably want an integration for a “read later” tool.
If it’s the RSS contents you might need to use a script or plugin in an existing tool, or just write something.
In terms of desktop RSS readers I like, RSSGuard, but currently using Akgregator.
Miniflux IIRC has integrations for sending things to “read later” tools like “Omnivore” but not many.
You might find something like mailbrew useful, but if you do perhaps a “send to email” is all you needed?
You could also publish content directly to imap and use the phone’s mail client which stores things offline too. (You don’t need a full setup for imap.)
Linux is a kernel, but people often refer to the whole thing as linux…
Everything else is independent free software, which without a distribution you would have to source yourself, configure, and install. Plus provide small programs / scripts to glue everything together. This same software can run on other operating systems depending on what it is. Unlike Mac and Windows, these are often by one vendor and highly integrated, less so with other operating systems.
KDE and Gnome, are desktop environments which are suites of applications, including a “window manager” which is the thing which draws borders, and allows you to minimize and maximize. Typically this is what non technical users think an “operating system is”
Distributions are highly varied in terms of the glue, and updates they provide. The idea is they keep up to date on the software and take responsibility (most of the time) for integrating it and ensuring that the configuration works.