I've never used flatpaks, but I don't like the idea of them simply because they are yet another layer of complexity added on top of an already complex system. The idea of compartmentalizing software components from each other as a security measure is an old but good idea. However, it really should be done on an OS level instead of as an extra 3rd party layer. If on the other hand, the purpose is not security, but to avoid dependency hell, then the problem should be solved on the package management layer by the OS, not by a 3rd party component. However, since Linux is not an OS, but just a kernel, a proper fix is likely never going to happen, so we get these weird middleware solutions like flatpak instead.
PS. Since I've never actually used them, I could have misunderstood the point of them completely, but OP's post seems to suggest that I am at least somewhat correct.