In the campaign guide for the mission Fly Solo, there is no round limit, and all heroes being wounded is not listed as a failure condition. The players also effectively control when the mission is over, so in theory, they could have as many rounds as they wanted to go collect crates, as long as they could efficiently deal with my per round threat gain.

I told my players this ahead of time, so they made full use of this knowledge and were a bit more cavalier than they normally would be. They conceded that it would be a PITA for every to stall the game to collect all the crates, so we punted on that =p.

Is this intended? How have others played out this mission?

The Mission Briefing section tells what the rebels need to know. It doesn't have a round limit for end of mission, so there is no round of limit. (There is no mission which installs a round limit later.) It doesn't give 'all heroes wounded' end of mission condition either.

The rebels still need to decide whether to advance the mission before the end of round 3 or let it progress automatically.