The *BSDs have all the same issues that Flatpak is trying to solve. (ports aint it.)

Flatpack also ain't it either. Sure flatpack solves a few issues, but it introduces others and so the problem isn't solve. Maybe it will be eventually (though the lack of maintenance implies it won't be), but today it isn't solve.

I found ports works very well myself - everything kept up to date with upstream, and they take care to rebuild everything all the time so you rarely run into library ABI issues.