PPAs can be a big problem. As a rule, I avoid them like the plague. I’m also the same way about unofficial Snaps not provided by upstreams, Canonical, or known developers. The big reason is because they don’t usually get the testing they need and the other reason is that they don’t provide any certainty of support.
However, I’m a little shocked a repo (it’s not really a PPA as it’s not hosted on Launchpad but even if it were, same logic applies) provided directly by an upstream is a problem. I use VirtualBox’s upstream repo every day at work and it’s flawless. There are reasons for this: it’s a primary and supported means of software distribution and as such, gets tested against supported versions of Ubuntu and gets maintained for them. That means it’s always working within the context of the dependency versions available in the Ubuntu repos, so these sorts of problems never exist.
Of course I discovered recently that QGIS changes the icon on JPGs, throttling over the chosen icon theme and instead plastering it with the QGIS logo. I realize QGIS has a legitimate reason to work with JPGs but this sort of behavior is rather ridiculous. It gives one the feeling that the default application to open a JPG is now QGIS. So either they know this and they don’t see it as a problem or they never bothered to look into the impact. If the latter is true, this may speak to their testing practices (or lack thereof).
Going back to VirtualBox, there’s another reason I like to use their upstream repo instead of the one in the Ubuntu repos: I can get support directly from the upstream. Many applications are used by wide swaths of users but virtual machine managers are not one of them. Furthermore, the developers and experts on VirtualBox are not necessarily Ubuntu users so they don’t pay attention to the Ubuntu bugs. So reporting VirtualBox bugs in Ubuntu tends to get a relatively slow and unproductive response (not a criticism of maintainers of the software in Ubuntu). Upstream, everyone contributing/involved knows the software intimately and uses it often. Bugs are answered quickly and definitively.
I say this because it applies here: there are a relatively small number of QGIS users in Ubuntu. All of the participants upstream are QGIS users. So I would expect any bugs to be dealt with swiftly and effectively. That said, since you’re using the upstream version, you should go upstream for support. I would start by filing an issue.
I also have a maybe unpopular suggestion? I see they distribute a Flatpak. Maybe try that instead since it will resolve all these dependency concerns. Or is there some compelling reason to not consider that as a viable solution?
One thing I will point out in closing: we, the Ubuntu community, are happy to help with whatever you try to do with your installation. That includes using software distributed directly by upstreams. However, we can’t guarantee support for such things in the way we can with the software distributed by Ubuntu itself. If you file bugs in Ubuntu against upstream software, it will usually get closed because of this. So do know that in using upstream software, you are removing the option of getting full support for it within the confines of the Ubuntu ecosystem.