I'm with Nigel here, Joe. It seems like the 100/90 Avons should work better on wider rims, but in the real world, I'm not sure you would notice the difference. I've been riding with them for a long time on stock WM2 rims, as have many others here on the forum, and they work just fine. And they get ridden very hard on occasion. I like the way the bike handles with them. It is very neutral feeling in corners. It falls into corners very easily, holds it's line properly, and doesn't push coming out under power. What more could I ask for on a street bike, except maybe better mileage on the rear?
As far as using the 90/90 on the front, I don't know what benefit you would gain from that. It would certainly work. I've seen a couple of Commandos with that combination, just never tried it myself. I raced several Commandos back in the day, and all had smaller front and larger rear tires. In fact my first race bike, a Commando PR came from the factory with 4.10x19" rear and 3.60x19" front.
Having said all that, if I were replacing the rims anyhow, and wanted to stay with the 19" size, I would go with the wider rims (in alloy, of course!). I can't see any drawbacks to following the manufacturer's recommendations.
Ken