I run Silverblue, so I have the Flatpaks of VLC and Celluloid. Both play MKV.
For me, it’s well worth running the Flatpaks so I don’t have to worry about codecs.
My first Silverblue system had RPM Fusion so the distro Firefox could play videos.
But since that makes upgrading harder (thought it remains very doable), on my current Silverblue system I “remove” (really just hide) the distro Firefox and use Flatpak Firefox, which like the video players comes with all the codecs.
I have plenty of space on my drive, and if I didn’t, I’d get a bigger one.
I don’t notice any lag on my 2017-era HP laptop.
tl;dr Flatpaks solve codec issues, and that’s one reason to try them.