I believe that in this case it's simply convenience/laziness to have a single notifications codebase across both operating systems? That and Windows didn't have native notifications when it was first developed. Not that it excuses a big chat application from MS behaving this way, just saying that they probably didn't deliberately choose to re-implement notifications just because they didn't like the OS ones.
Windows has had balloon notifications since Windows 2000. These show up as toast notifications by default in Windows 10, so compliant applications would be transitioned automatically.
Some software also presents that in the settings as the choice between "native notifications, which don't have as many features" and "custom notifications, which have all bells and whistles". And the default of course is the one with more features, not the one that respects your settings. I think Mattermost was where I've seen that distinction.
This is what happens in an Electron world. Lots of experts around to make some JS+CSS notification boxes because they keep reinventing those for every SPA anyway, but.. integrate with the native system notifications? They don't even know how Electron works so how would they begin to do any of that.
