The difference is usually more like "software A requires an hour of setup and constant maintenance on a dedicated VM or container due to dozens of dependencies, and software B requires 3 clicks"
Case in point, I recently upgraded the computer of a non-technical person from Ubuntu 18.10 to 19.04. And now desktop icons are completely broken. It's been reimplemented in JS, with horrible performance, and doesn't even support features like dragging an icon to a folder. Their reason for removal? A bunch of technobabble no user would understand. https://gitlab.gnome.org/GNOME/nautilus/issues/158
When stuff gets removed or shut down, the basic reason is that it takes work to keep it going, and someone decides to stop allocating any work to that. Even with client-side software with no service to run (like that mobile app), the platforms they run on change, and it takes work to keep up.
And that's exactly what I see in that GNOME issue you link to. There's a bunch of technical detail about why it's so much work -- but the point they're making is it's been a lot of work to keep that feature going the way it was, and it'd be even more work to continue doing so as the rest of the software on the desktop changes around it in the ways that are planned. And so they decide to drop the existing thing and build a new one in a much easier way.
The only difference from proprietary software is that everyone has the option to step in and say, no, I'm going to go pick up that work, and everyone's welcome to use my version instead. In fact, GNOME makes a great example, because there have been a bunch of popular projects precisely about doing that with previous decisions they've made: https://en.wikipedia.org/wiki/Cinnamon_(software) is one of the bigger ones.
If people had that option with Google Reader, it'd be alive today. (I'm told it was a very small amount of work to keep running, and when the ax fell on it many Googlers pleaded to be allowed to just keep it running on their own time.) Ditto for many of the other proprietary things I've missed after they went away.
Stuff does not get removed from proprietary software installations spontaneously, unless there are automatic updates (which can be turned off).
Stuff spontaneously disappears from a proprietary website, and the users can't do anything about it.
Proprietary websites are a whole new form of social harm that makes plain old proprietary software look virtuous in comparison.