Why it's an issue is, why a five year old rule has only just become an issue isn't. It's not specific to mtn biking, it's all UCI registered riders.
I think the issue is that the rule has always been interpreted as applying to (members of) UCI-registered teams, not to all licensed riders - this is how the US cycling authorities have interpreted it and this is what they have told riders. This has, up to now, apparently been fine. But this year the UCI decided that they would not allow this interpretation and that the rule should apply to all licensed riders. In the MTB world, this makes much more of a difference than in the Road world because there are a lot more independent events outside of the UCI ambit, and a lot more riders who ride both UCI and non-UCI sanctioned events. That's just how the MTB world is. The way I see it, this is about the UCI trying to assert control over the MTB racing world. I mean, why should it be the case that a rider who holds a license to compete in certain kinds of races is banned from riding in others? A license gives you the right to compete, it is not a form of indenture. This rule, particularly in the recnet official (re)interpretation, is unecessary to anyone else except if you are a UCI official who thinks that there should be nothing in cycle racing that takes place outside of its control. Luckily they seem to have realised that the MTB world does not buy into this vision. We'll see what the next move is...