I think the main reason why the directory exists is that files in there can be owned by packages. Otherwise, scripts would have to edit the global file. Scary. Note that if you would manually add the TV repo to a different file, you would end up having it twice, which is not a problem unless you edit/disable one of them and look confused because it does not have the desired effect.
Before or after 3. you might add Flatpaks. It’s basically just a different kind of package/repository. For some, it’s also controversial. Please keep the flaming in this thread.
Purism embraces it as a way to enhance the system with apps that are not (up to date) in the repo.
I did not mention it before as it will most likely not help you with the problems of those ecosystems with their own package formats you’re dealing with.