Others have mentioned disk usage and desktop integration. There is some truth to them, but shared runtimes keeps disk uasge down (although worse than native apps). Desktop launchers now search /var/lib/flatpak/exports/share/applications by default, but I'm still having issues with themes in one or two niche apps.
Trust is the big one. The benefit of your distro's packages is that they are maintained by a limited number of maintainers. Flatpaks have a much, much larger number of maintainers, which is where sandboxing comes in. Flathub now marks apps with lax permissions as "potentially unsafe", which is a huge step in communicating this to the average user.
Most desktop apps can get away with having next to no access, as long as they support the appropriate XDG desktop portals.
Ultimately, your mileage will vary, as there are many classes of application which are ill-suited to being sandboxed. Program launchers, programming languages, IDEs, file managers are a few.
I used to use Strawberry, but my collection has grown enough that I can't just sync it everywhere, so I use Jellyfin now. I still use Strawberry's library management to move files into album artist/album/00 - track.ext though. Someday I'll dig into id3v2 to just write a script instead.
Its incredibly common to be thrown by this. Like many memes, the original incarnations were to be taken at face value, but then a layer of irony got applied, and the ironic/self-deprecating variant became the norm.
8GB memory + two Firefox profiles makes things difficult on my laptop.