If mods were probably written this wouldn’t be necessary at all.
Well, users deal with the mods there are, not the ones they wish they had or should have. It's good to talk about how things ought to be when we're laying out a foundation for a future platform, but it doesn't change the fact that many, perhaps even most, mods don't actually work this way in the present. If time spent unnecessarily uninstalling and reinstalling everything can be saved now, I don't see why that should be avoided on the grounds that the problem shouldn't have come up to begin with.
It’s also reliant on mods being correctly installed first time and no manual edits taking place, and implementing it would break some mods that already exist.
If the installation was broken, though, you
already have a problem, and will whether you have access to this or not.
As far as manual edits go, the current system of uninstalling every single thing and reinstalling it all over again isn't any better. In fact, this is an improvement in that area since there's the possibility that the changes to other themes aren't that substantial (adding a few image files or tweaking a couple of lines of CSS), just tedious to do by hand.
For existing mods, I'm unaware of an example of this and would like to be clued in; if they don't affect the package manager, I admit it isn't clear to me how it would break them.
I'm not trying to be rude or antagonistic, and I apologize if I've come off that way. I just don't see at present how telling the package manager to not do anything except a step that seems to be already separate from the rest of the process (enough so that you can choose to omit it, without any ill effect) is worse than leaving the real inconvenience it's attempting to patch alone.
Now, if changing the other themes
isn't an isolated step, contrary to what the GUI seems to suggest, then I could understand the hassle here. I'm not aware if that is the case or not; if it is, I'll certainly stand corrected.