BMW MSRP on the tranny is $5189, so that part is typical profound exaggeration for what aim is anybody's guess.
When I first read your post, I assume you were talking about rollover noise which is normal and common in a small amount (clutch engaged, transmission in neutral). I'm talking about the kind of transmission noise you hear with an aftermarket clutch in many cars with dual mass flywheels where the flywheel has been changed for a single mass design (although not nearly that loud, just the same noise source).
However, if the supposed experienced tech doesn't think it's normal, I have no clue what that could be. If the transmission is ruled out, that leaves only one source - engine. If the noise is in fact rollover noise (engine at idle, clutch engaged, in neutral) and is verified to be coming from the transmission, I would simply hope they have already put in a complete new clutch kit (flywheel, clutch, pressure plate, etc) as if the dual mass flywheel has weakened springs/damping, that would enhance transmission rollover noise...
Does it sound like a clattering (trans in neutral, clutch engaged) noise from the transmission? (as opposed to a bearing whine)
2011.5 M3 sedan 6MT, Silverstone, no sunroof, no EDC, but most other options
2001 M5 LeMans Blue/Silverstone
2006 330i 6MT Red/black, ZSP, Nav, etc.
2001 Audi S4 6MT; 1996 Volvo 850R wagon