possibly will break flatpak in: [...]
- NixOS - is everything cool and happy on NixOS in that case? I would be cautious.

NixOS uses systemd extensively and adding services is trivial. I'm sure it'll be fine.

In fact the Gentoo userbase of Flatpak is rather large.
[...] main reason [...] is to get Steam running

Flatpak has been really useful to me on Gentoo for various reasons:
+ Steam on a (no-multilib || musl) system;
+ not having to compile huge projects that I don't use often;
+ testing out desktop software. (otherwise I use nix/guix)

I suspect the same thing could happen as with systemd-logind, i.e., the systemd-specific parts being extracted to a distro-agnostic solution (elogind in that case).
The only reason I see for not making it distro-agnostic from the start is that it's easier (for them) to target systemd.

CC: @xgqt@functional.cafe @kimapr@ublog.kimapr.net @LAS@floss.social @jorge@hachyderm.io @2something@transfem.social