As for being overkill, surely you can see the advantage of having a single uniform distribution format from the end user's perspective? Which, sure, might be overkill for your case (although app isolation isn't just about dependencies), but the important thing is that it is a working solution that you can use, and users only need to know how to install and manage them.
You have to install the flat pack runtime to begin with so that’s one obstacle for distribution. And it also doesn’t really isolate as much as you’d like to believe - eg dealing with audio will still be a mess because there’s like 4 different major audio interfaces. And now I have to host a flat pack repo and get the user to add my repo if it’s proprietary software. It’s really nowhere near as smooth and simple as on Windows/Mac/Android/ios.
The reason to host a repo regardless is to enable easy auto-updates - and I don't think you can call this bit "smooth and simple" on Windows and Mac, what with most apps each doing their own thing for updates. Unless you use the app store, but then that's exactly the same as repos...
As for being overkill, surely you can see the advantage of having a single uniform distribution format from the end user's perspective? Which, sure, might be overkill for your case (although app isolation isn't just about dependencies), but the important thing is that it is a working solution that you can use, and users only need to know how to install and manage them.