It’s fine. No real crash/stability issues on the flatpaks I’ve installed. The real downsides are that, yeah, some apps don’t integrate well with the rest of the system either in some functions or theming, due to the sandboxing, and if an app has many or large dependencies it can take up a lot of space compared to a native/repo app and you also may then have more than one copy of those dependencies on your system. That doesn’t usually cause conflicts (a positive side of sandboxing), but it may be a problem on smaller storage devices if you use a lot of flatpaks or need other large apps installed.