I see a lot of burr knots around the base of some trees on MM111 rootstock. Today I covered up some on a few trees with dirt because of the issue you just mentioned about it being an entry point for disease and pests.
I had never seen any knots high on a tree until I got some of the NWC crabs last year. Two of those trees resemble his picture above, but I don't see any open places like they look on MM111 rootstock down low at the ground.
When you have them down low near the ground, I think the best thing is to cover them with dirt.