An interesting question, and I'm afraid I don't know the full answer.
There are some differences that happened with the XT600 model from 1990 that changed from the earlier and more compatible model to our 3AJs, but I am not sure how they are material?
The design of the front wheel shaft and fork fixing changed, eliminating the need for a lock nut & cotter pin. Whether any of the dimensions changed I don't know? However they could have as the Wheels changed at the same time - the front rim became wider, and the rear wheel size went down to 17".
I have a copy of the Yamaha '90 model guide, and it notes that the Front & Rear Wheels are "not interchangeable" between the '89 and '90 models, but it gives no hint as to why.
Have you thought about new rims using your existing hubs? I guess this is more expensive than the 2000 XT600E wheels you are being offered?