UTC is typically used for co-ordinating flight plans, air traffic control, and so on, for precisely this reason. UTC is 'standard' time in the sense that all other timezones, including daylight-adjusted ones, are set against it.
Of course, UTC is typically not used in day-to-day use by the public, so times in timetables, etc., will still typically be shown in local (daylight-adjusted time). In your examples, the only unambiguous way to express 2.29 when it occurs 'twice' would be to append the timezone identifier (for example, the UK uses GMT or BST, depending on the time of year). It isn't a problem very often!
I have flown from the US to Europe before during a mismatched week (the US adjusts away from DST a week before Europe). It wasn't a problem; the local times were just adjusted accordingly on the tickets, airline website, etc.