*Caveat* (This is not an attempt to diagnose your issue)
I once had a similar conundrum.
an amplified whining noise under acceleration after a 6 speed manual box in my 124 coupe.
I was absolutely sure it wasn't the box but the noise was absolutely saying everything otherwise, and to experienced specialists.
It had new engine mounts and geabox mount, and the geabox crossmember had been meticulously strengthened to cope with the tiniest of grabox mount repositioning (6mm forward of previous location and different pilot holes for bolts)
So, with a complete new shifter assembly already thrown in just to ensure it wasn't in linkage bushings etc, and the propshaft checked and balanced (nothing changed) set about absolutely convinced now or never, the box was coming out again.
Took it for a drive and the noise was there, but  swapped to passenger side and let mechanic drive, and armed with a stethoscope, decision was "yep, has to be gearbox".
Put up on the hoist, and just as we were getting set to pull the box, suggested another look from underneath with it running.
Mechanic got in, hoist up, in 4th and applied throttle. Said he could hear the whine and as he clutched in I thought I saw something...
asked him to repeat.
and there it was.
the rear gearbox mount (brand new) had a completely invisible separation of the vulcanized rubber from it's alloy encasement, and because of it's design, rotated under load just barely enough to transmit the engine and gearbox vibration straight into the crossmember which essentially was directly behind the shifter inside the cabin.
Replaced the gearbox mount with another.....
noticeably less rotation, and some more violent clutch actions on the hoist confirmed problem was likely connected to the mount - but we still weren't confident.
off the hoist and a test drive around the block with a few "race mode" launches and a couple of highway blats and back into the shop on the hoist to check the mount and everything else underneath.
While the noise was essentially much quieter, there was the faintest bearing noise, and it was soon determined that the tiny little insulating washers between the crossmember and mount were omitted.
reeplaced them and ALL noise was gone.
absolutely nothing wrong with the gearbox - but we scratched our heads for nearly 3 days solid trying to work it out while avoiding the removal of the gearbox (because it's a pain in the ---)
so unless you're convinced beyond measure, and can get it on a hoist and much around with a stethescope probe on all the 'areas of concern' I would hesitate to say it's the box, even if you have a professional standing beside you arguing until they are blue in the face.
Show them this post if they still aren't convinced. then go back to troubleshooting 101 and the process of elimination - because it is the only way to successfully diagnose a noise that "is of concern" but is not able to be easily located or distinguishable from other nearby interefering noises of a similar type.
old mechanics screwdriver stethoscope is a great tool for isolating clunky things inside engines, gearboxes and diffs. 
It's just more time consuming and difficult without a hoist.
Hope you find your issue is an insignificant one. (read inexpensive)
				
			 
			
		 
			
				
			
			
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