Well, thanks everyone for the response, I had another go at burying them and they somewhat stay buried now, dug as much as I could and then put a layer of wooden floor and on top of that a layer of stone floor

They sometimes still pop out a little bit but I'm willing to put up with it until devs implement a way of deleting these rocks... hopefully

Also, they were somewhat part of my build but I ran out of space since I built my base at a shore, everything was crammed together because of these rocks and I finally got tired of it