Strange. So far I cannot remember having a notification not disappear after clicking its card in the updated window.

Sometimes they do, sometimes they don't. But mostly they disappear promptly after I've checked the changelog in my library. Maybe the notifications are bound to some offline website data which sometimes does not refresh often enough.

My hassles are that changelogs or notification appear sometimes hours after the game itself updates via Galaxy. I would like to know the changes to my installed games immediately.

Also it would be nice to read Galaxy update changelogs without having to look in the forum.

Ok I am not 100% sure if it would clear the flag also by clicking somewhere else (maybe I misunderstood you that you just open the gamecard)... but to me at least those two seem to be sure ways to clear the update flag, either by checking More => Changelog (if available), or starting the download. Even then it might not clear it instantly, but pretty soon anyway (within a minute? Sometimes instantly maybe.).

Maybe this will get you started in Windows:

https://www.gog.com/forum/general/is_gog_downloader_still_supported_by_gog_or_are_they_scrapping_it/post39

I think Python 3.5.x is nowadays fine too, it doesn't have to be specifically the older 2.7.x (I have only python 3.5.x installed on Windows). On Linux, setting gogrepo up is even easier as Linux distros usually seem to have python already installed.

One thing that was missing from those instructions was that sometimes GOG seems to have been forcing captcha when you try to login without cookies. That would make the "gogrepo.py login" command fail as it can't handle captcha.

I am unsure if GOG is currently forcing it. If they are (and gogrepo.py login doesn't work), then you have to do a workaround, e.g. in Chrome or Firefox log into your GOG account successfully (passing captcha if needed), and then use some Chrome/Firefox plugin to export your valid GOG cookies for gogrepo.

I don't think captcha is forced at the moment so the login should probably work right now, and either way the good news is that you need to pass the gogrepo login only once. After you have valid cookies for gogrepo, you don't have to do login again (as long as those cookies stay valid).