I've been unable to tell whether time spent flying from location to location counts towards any of your own timers (research, construction, healing, etc.). That is, I've never had a project finish in midair or upon landing, even though some trips seem to take upwards of half a day. Does it affect any countdowns? It seems like it might still move time forward on alien actions, but I haven't noticed one way or the other.
(note that it at the very least affects achievements, assuming the "Exquisite Timing" achievement for beating it by July 1st works as described)