I wouldn't be overly concerned about the root issue. JM's seem to have or develop this issue somewhat frequently. I discovered similar crossing or odd root alignment on several of mine - grown in containers - when I have had occasion to root prune and repot.

Cutting the root is more likely to create a favorable environment for verticillium wilt than leaving it intact. At this time of year I wouldn't mess with the roots at all.

Ok. Can diseases go through the bark flaking as well or is that only if the cambium layer is exposed?

They could.....but they usually don't. Generally, it's the other way around. Some internal pathogen causes the bark to flake off. As long as the wood is firm and dry where the bark flaked off, I doubt you have anything to worry about.

Again, I have encountered similar situations with my own trees and it was a non-issue.

If the tree is healthy, there’s nothing to worry about.