I would think that the Goths do get a penalty for taking the wrong flight. Like "You were meant to ride the 9:50 A.M. required flight and did not, and for that you have received a 30 minute penalty." For example, Brian and Ericka in Season 15 walked on foot to the Detour location (I think) in the Netherlands rather than taking bikes. They didn't gain any time (it actually cost them quite a bit of time) but they were penalized for not following the rules.
So I would assume that you get a 30-minute penalty for doing something that you aren't supposed to do, including taking a different transportation from the required one, regardless of whether or not you gain time from it.
Also when Justin asks Kent "So you didn't take the flight that we were supposed to take?" I think it's foreshadowing something... xD