I have never had any experience at travelling with a 3D printer. However, I think having its own case is perhaps the best option. Could you buy a suitcase, fill it with padding and keep your printer in there and just use it like another piece of luggage? I know you have concerns it will be tampered etc but this would probably be an issue with whatever method you choose?

Out of interest, judging by your user name I am guessing you have a Subaru? Excellent cars - I would love to own one some day!