I think the "issue" isn't the package manager overwriting your custom unit files, but rather just the litter of untracked files in places the package manager is supposed to be in charge of. Since some people want to be able to track those files, and prevent them from making a mess.
In practice I don't think it is a huge issue. I've just left unit files laying around on embedded devices without issue. Hard to find which ones are mine though, if I've lost my mental list of them.
(Also, writing one from scratch without a template is annoying, since I haven't memorized the format.)
You can even do this with 'systemctl edit <unit>' and it'll create a file in the right place for the override and show you the original contents for reference
In practice I don't think it is a huge issue. I've just left unit files laying around on embedded devices without issue. Hard to find which ones are mine though, if I've lost my mental list of them.
(Also, writing one from scratch without a template is annoying, since I haven't memorized the format.)