The Yamaha tech you talked to is wrong. Yamaha is STILL installing this bearing with the seal towards the oil. The crap from the track is kept out of the bearing via the LIP seal installed in the case where the driveshaft goes through the back, before going through the bearing. The other bearings are open because they are not immersed in oil and have a greatly reduced chance of particles settling out in the bearing while the sled is stationary.
I change the oil every 1 to 2 seasons using a synthetic 75/90 gear oil.
The old man's Vector GT went 11,500 KM on the original bearing and we only retired it because we were in the case to change his track.
I'm only posting this to 'clear up' any mis information, you're all welcome to do what ever you like in regards to your lower chaincase bearing, as Blue will attest to, both ways seem to 'work'. The chaincase bearings are the cheap ones to replace if you catch them before explosion. Be sure you are servicing the clutch side bearings as well (jack and drive) by greasing, either by removing the seal or using a grease needle.