I have my Synapse 3 serviced at a Trek/Specialized shop and have zero issues with tune-ups, cassette changes, etc... Trek uses a lot of proprietary parts (Bontrager is owned by Trek) as well but I am guessing your concern is the integrated Cannondale headset? You don't usually need much maintenance on that part and if you like the shop selling it then they would be able to service it. We do have a Cannondale shop that can handle warranty issues since the one I bought from closed down. So IMO your concern about proprietary parts won't be an issue.

I would ride both and see which one you like. I would put some consideration into the drivetrain but how they feel is a much larger concern. Cannondale has an excellent rep for honoring warranty, I believe Trek does as well so you can't really go wrong there. Carbon is not like riding a glass bike, just make sure they go over how to care for one before you buy.