Huh, I have/had a relatively similar setup. I'm also using Orgzly and if I want to look at a file on desktop, I open it in Kate.
I don't tend to edit those notes on desktop, though, partially because I just don't really have a use-case for it, partially because I've had sync issues when editing on both sides.
Similarly, I rarely need to access my desktop notes on my phone. If I do ever have a thought to add, I just create a separate note on my phone and later add it on desktop in detail.
Well, and then because I also have more of a need for Markdown nowadays (every so often I get to copy something verbatim from my notes into an external Markdown system), my desktop note taking system has kind of drifted off towards that.
Certainly would not mind a Markdown app with notifications either, but the problem is that Markdown has no syntax for adding dates, so it could at best be some non-standard format, which would likely only work in that specific app...