Lets look at a few things here. You "need" to break in an engine to refine/hone the piston rings to conform with the cylinder walls. That's about it. The bearings/crank/rods don't actually touch each other and are separated by a few thousandths of oil film. On a performance rebuild with hard rings, the idea is to run it in hard because the walls will have a slight texture from the final hone which will sort of file against the hard rings. Works great. 20 min idle then straight to the dyno at low boost. Then there are cars like the Z06 where break in is done for you at the factory, so you can lay rubber at redline right through GM's parking lot on the way out.
Transmissions are different. They use roller/ball bearings, which shouldn't need any break in. The gear meshing should be checked at the factory so I don't think it would need any real break in save for delivery miles. I'd be more concerned about the clutch/pp/flywheel break in, like you should be familiar with on any new clutch. That's more for holding power though.
I mean, consider this: most people debating in this thread have pulled a magnetic trans plug on a stock FS5W71C. There's not a whole lot of fuzz on it after 100k+ The whole idea of a break in process is to refine the mating surfaces. That means removing material. At no point in this process does anything magically become stonger. We're talking about longevity with regards to wearing out, not catastrophic failure.
I know what this is about. It's about that GT-R transmission. It just has weak clutch packs. No one is talking about gears exiting the case or being stuck in "neutral", etc. We're talking about losing the 1-3-5 or 2-4-6 gears. These sets have their own clutches. When that clutch fails, you lose that set of gears. As far as a clutch drop, you can't really do that in a GT-R. It slips the clutch for you. The problem with dropping is shock loads. The GT-R trans is on a carbon driveshaft that will have some deflection, and is on a rubber isolated subframe. Compare this to a traditional setup where the trans is bolted directly to the engine and crank where no deflection can occur. And the problem with shock loads is breaking gears. I don't think anyone is breaking gears here.
Nissan's 20k trans.... That's because they're Nissan and won't open it up to fix the broken bits. The entire transaxle is 20k. They did the same thing with VQ35's that drank oil and FS6 trannys that grinded. In both cases (rings, synchros) the fixes were less than $100, but they would swap whole assemblies. Do you think any dealer wrench (with or without 12 hours of GT-R slideshows, er training) could sort through a tranny like this? Best case would be FedExing it back to the BW factory. I think part of this is making an example of idiots who break things after a week, and setting precedent. This is just Nissan saying that they won't fix every idiots tranny for free because they like to show off. People seeing failures in normal or spirited use should be getting freebies.