Hello, I’ve read through some of the other forums and see that things like the N’sane trilogy are not allowed, but I’m curious about the NSO versions of SM64 and BK, are those allowed for runs?

NSO versions are fine. What is and is not allowed version wise is dependent on what's accepted for the single series run. For mario see the 602 rules, for Sprash, see the 642% rules, for rare, see the 301% rules

Because NSO is allowed for 602/301 runs on the SM64 boards and the BK boards, they are allowed here. The same cannot be said for the Reignited Trilogy / NSane Trilogy.