I don't think so. Its going to be extremely hard for M$ to try and change the media format for games in X360 now. Even if they factory integrate X360 with an HD-DVD drive, you'll still have to force all 5mil+ customers with X360 right now to buy an HD-DVD drive just so they can play the games. Which will backfire like nothing before. People aren't ready to buy a Ps3 just because it includes a Blu-Ray drive which bloats the price, they sure as hell would rather give up their X360's and buy a Ps3 than to get the HD-DVD upgrade.
In any case, I don't think the 3-disk editions are going to be any problems. X360 players are trying to justify the scene by bringing in FFVII. It too was released a year or two after the Ps1 released, and also packed 3 disks. If it wasn't a problem then, it won't be a problem now.