Good question/observation to which you will probably get many varied answers. Only Mr Yamaha knows the full answer. Do not forget there are engineers out there who have made (and sell) improvements to this bike and its engine. Alternatively a PhD paper on the XT 600 might unearth the whole story.
Yes, the 3aj some upgrade (oil pump inpaticular) which explains the extra oil line, thus giving greater lubrication to the gears. The gears have been upgraded but I think you will find that this came later in the 4pt and these you can (so I understand) be fitted to your and other earlier XT's.
When it comes to the gears, the problem is greatest with the 5th gear, but includes others. this is mostly due to the abuse inflicted whilst in 5th at low engine revolutions, combined gear change (stress). If you look at updates on later XT's the clutch housing changes to the right of the bike!
The colour of the engine (it is suggested) makes no difference other than the colour, it is said. However I think that it unlikely.
I suspect this is not the answer you seek. Yet I hope it helps.