Fedora and Ubuntu use different versions of GTK, and that actually affects the behavior of the notification area. They also probably use different versions of the sni library.
There’s also the issue that Ubuntu ships with indicators whereas Fedora doesn’t. That also affects how/where some tray icons show up (and their behavior).
The bug reports are helpful, and the mate devs have been working on this particular issue for a while. Part of the issue is that notification icons are actually no longer supported in GTK, so fixes and updates to the underlying libraries are a non-starter, so for now it’s mostly hacks and workarounds until a new solution is found.