Severing them will cause the severed roots to rot, but rot in viable tissues would have to be caused by something other than being in close proximity to the rotting severed roots. If you have an organic component in your soil, and certainly most do, it is constantly breaking down from decay, so the decaying of the severed roots is nothing new.

If, however, the mass of the severed roots is large enough that the decaying tissue clogs soil pores as it breaks down into smaller pieces, the anaerobic conditions it would/could create could possibly create a cultural setting in which harmful fungi/bacteria could develop.

Al

You could remove it but the other option, unless it's an ugly addition, is that the more large roots you have on the rock the more stable the tree will be.

If you decide to keep it I'd suggest padding the roots with something like innertube rubber and use a few large cable ties to slowly ease it in until it's touching the rock. Just snugg it up at first then slowly add more pressure until it's pulled in.

Bob