It is probably an old case design. In the early water cooling days, there would be separate watercooling units that sat outside the case. The grommets were so you could pass your tubing through.
I wouldn’t really worry about the dust tbh, you will wind up having to clean it regardless.
My primary machine is still Windows, but pretty much all of my other machines run some version of Linux. The only reason my primary is winows is because I do a lot of 3d modeling and gaming. (Yes I own a steamdeck and it works really nice, but some of my fav’s still refuse to just click the “let anticheat work on Linux” button.)