Are there any perceived or non-obvious disadvantages to option #2?
--None that I can think of. We would still be able to do everything in Pro Tools (embedded Settings, re-amping etc.) and the standalone app would be designed to run alongside Pro Tools if desired. The actual user experience shouldn't be all that different.
Would option #2 require an iLock dongle to launch? - i.e. is it _that_ separate from ProTools?
--No. The app would not require an iLok
