I was told the
portion that goes into the emt needs to be unsheathed, per code

That was never true. Actually using a cable this way is violating the listing.
A cable is an assembly and designed to be used with the sheath on.
I am also not sure where the derating rumor came from. Derating is based on the
number of current carrying conductors grouped together ... period. 4 or more
current carrying conductors are derated the same if they are in a cable, a 1/2"
pipe or a 4" pipe.
With a 90c conductor it is pretty hard to come up with a case where derating
will affect NM-b anyway.