Yes, you can use RW on both computers. You can even share the addons folder, although some folks have had issues with Dropbox and OneDrive synchronization, sync.com or iCloud seems to still work okay.
As for using Migration Assistant or doing a clean install goes, from a RapidWeaver perspective, I don’t think it matters. Other than forcing you to do some ”house cleaning” by not installing what you don’t use anymore, clean installation really won’t buy you anything.