I found some information regarding removal of knees, I assume it also applies to permanently covering them up
According to LSU
horticulturists, you can carefully remove the knees without harming
the tree: Dig a small area to expose the knee a few inches below the
soil level. With a clean, sharp knife or saw, cut the knee off
horizontally, 1 to 2 inches below the soil level. Refill the area.
Texas Forest Service's Mickey Merritt assesses knee removal as he does
root removal. "It depends on the size of the root that will be cut,
how many will be removed and the distance from the tree," he says.
Merritt has removed small knees as they developed from a 35-foot-tall
cypress in his front yard. These have been about 60 feet away from the
tree, well beyond the critical root zone. (The critical root zone is a
circular area with a radius of 12 inches to every inch diameter of
trunk, taken at 4 1/2 feet above the soil level.)
If there are a lot of knees. he suggests removing them over a couple
of years and, if possible, staying out of the critical root zone. If
this is not possible, it's important to make clean, smooth cuts and
not chop, rip or pull the knees.
Some gardeners do give up the lawn and add other plants - or just
mulch the area.
Trees for Houston's Matt Weaver does not recommend removing cypress
knees. He says even though bald cypresses are tough and usually
tolerate this practice, it will stress the trees like any mechanical