Look, you're not going to find something that satisfies you.

The best you can do is a directory full of plain text and markdown files stored on a Dropbox or something.

Then, on Linux use something like nvpy or one of the numerous text editors. Point it at the Dropbox dir. Write a bunch of helper shell scripts to automate tasks.

On Mac, use something like nvAlt and point it at the Dropbox directory. Or go do the same thing I mentioned for Linux above.

On Android, find some plain text notes app that lets you point it at a Dropbox folder.

If you're into a cloud-based solution, take a look at Simplenote which has clients for all of the above.

Don’t like proprietary formats. So I’m using plain text with a markdown editor (Typora on Windows/Linux and iaWriter on Android iOS/Mac sync via Dropbox. One file for work and one for private notes. I store references in zotero. You even could use zotero alone. If I need to export to pdf, html or slides i can use pandoc. I’d love to use orgmode/emacs but i just can’t remember those shortcuts.

You could probably jerryrig "seamless synching" with some initial effort simply using VimWiki and git, of course the Android portion is going to require the most significant setup, but I don't see a reason why it wouldn't be doable (but then I'm not too familiar with Androids filesystem and I'm assuming it works at least marginally like the Linux filesystem)

Have also used Joplin. Although used this more as a personal wiki, e.g. relatively long-form notes. I would read it on mobile but rarely edit. Agree the sync there is 'clunky'.

Microsoft OneNote is quite nice.

But what I actually use most is all the Google products: Keep, Docs and Sheets. So, native app on my phone and then browser based on the laptop.

Have used OneNote in the past, but I guess there's no Linux client?

Simplenote syncs between Linux and Android, but I don't know about Mac. It is also truly simple and lightweight.

It works just as well on Mac too, no markdown support though..

Emacs with org-mode (desktop) - Orgzly (very well integrated into Android) - synchronized via Dropbox

I use workflowy. Its webapp works on any browser and it sync in real time.