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.)
ah. Sorry