That is a good reason. Another good reason is that the files in /usr/share/applications will get overwritten when the package that owns them updates. I agree that modifying those files should by no means be common. At least, not on an Arch-based distro.
Depending on what boot manager you use, you may need to edit files in your efi partition which is commonly mounted at or under /boot. It still shouldn’t happen that often though.
For some reason as yet (to me) unexplained, the override does not happen on my systems. So, I have to overwrite every update - to the point I have a script for the purpose. Not just changing the icon, but also the resolution and other things…
I also have quite a few things I edit in /boot/efi/EFI - partly because I use rEFInd. That also leads, sometimes, to things that need editing in /boot itself. I also find myself moving/copying etc things between distros, rather than re-inventing the wheel…
I am not recommending this methodology to others, but with the tools I use it has proven reasonable. Another ‘trick’ I am looking at is instead opening a root terminal from Thunar at the current location, which should have the same effect with fewer potential downsides - and I can switch to micro for editing in root mode - once I get a satisfactory syntax highlighting going for the file types I edit so often 
Well, it’s not my place to tell you what to do, but I would look into finding a proper solution to the problem, rather than use a workaround script.
I have been looking for a reason for this behaviour for some ttime, so long, in fact, that it’s priority has dropped considerably along the way. Perhaps I should again pick up the search for potential reasons - it is just hard to give up something that has worked well for so many years 
Have you any thoughts on the direction to start checking in for this problem - as it has persisted across several distros and distro types for a LOOOONG time. It weould be so much more ‘elegant’ and easier if it functioned as described…
Are you sharing a home directory across all of those installs? If not, are you positive you are using the correct path in a case sensitive manner. Lastly, how are you testing?
I do not share the /home directory - partly because of the possibility/probability of problems with differing distros, and partly because it would be of no benefit. I already share data across the lot - soft linking the ‘standard’ directories (Documents, Downloads, Pictures etc) which neatly handles any benefits a common /home would give me (that I know of!).
Testing has been limited to altering icons, Exec= statements and so on in the ‘override’ directory - and having the changes ignored. Is there any better testing regime, given that override is what is desired?
I do the same. Some people like all their .config to be shared but I prefer those to be isolated for each install/distro.
I don’t remember what it takes to have those changes be effective. For example, is it instant or does it require logout/login.
I think it depends on the DE. At least on KDE it’s pretty much instantaneous.
I’m not sure it makes much difference whether a logout/in is required. I still have the ‘correct’ files in ~/.local/share/applications - and they still get overridden on every update. It is only knowing that they SHOULD work as described that has kept me throwing in a pacman hook to automate the process of ‘correction’!
I guess I should put it down to a habit of ‘making it work’ taking precedence at times over ‘making it work right’!
BTW - with the number of reboots that get done with this setup, it should worked once by now!
Very strange… Try making a new user account and see whether it works there. 
http://www.linfo.org/kdesu.html
Edit: I try it and it doesn’t open locked folders in kde?
Have you read the whole topic?
No … 
Edit: It’s very confusing …seems to be talking about different things. I don’t do a lot of changing ownership and such. I would just also like the ability to open a folder in dolphin and make changes like i can in Cinnamon with nemo. Can’t do it easily with Dolphin or Thunar. Just looking at kdesu as i never heard of it before.
Maybe go through that first. 
I just thought it would work like sudo thunar does. It comes in handy for just simple things if i want to remove a folder or something else.
Tldr: ‘kdesu dolphin’ works exactly like ‘sudo thunar’, but only on OpenSUSE. It doesn’t works on EndeavourOS or many other distros for stability or security reasons.
Next time I try Open Suse KDE then I’ll give it a go.
Does it have to be Dolphin? Krusader is a better FM IMHO and it has a root mode.
I use konsole almost exclusive for root owned files, to edit one I just use the se alias I mentioned above, which launches kate as sudoeditor. Much quicker usually, particularly if you know what you are looking for.
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