yes, but the theme is going to be less universal because the stock rom is odexed. but as a side note odexed roms have faster boot ups. so you'll be able to get a hybrid with your stock rom. fast boot and a themed rom. you should check out the "blackglass theme for odexed Droid 2"
you're not gonna want to deodex the rom yourself. You're going to want to find a deodexed Rom and flash it. But then you are Adding a custom Rom that you didn't seem to fond of in the OP. So to answer questions. Yes you can theme a stock (odexed) rom, but it is limited theming. Deodexed Roms provide the ability to do complete theming, but you have tyo flash a custom deodexed Rom. There are Deodexed Stock Roms floating around if you want one though.