How can I bend 180 degrees over a duct trunk with height restriction?

There's no rule that all your bends need to be plumb and/or level - these things flex for a reason.

Move the start collar to the left (in the picture). Rotate it so that instead of making a 90° straight up, it goes up and to the right. Make your next 90° continue that "up and right" direction until it clears the top of the main trunk, but doesn't hit the ceiling. Wiggle & adjust until you have satisfactory clearance from all surfaces.

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Thinking more about it (and to be abundantly explicit):

I'd connect the two elbows to make a "straight" 180° turn, then push it up against the trunk line toward the left of the joist bay and "lay it down" toward the right until it cleared the floor above^*. If you want/need the take off to run down the center of the joist bay, the take off from the trunk can be under a joist above or even in the next bay over - there's no rule about that, either. Once you've got it in a "safe" position, mark the screw holes, cut the appropriate openings and fix it into place.

I'd do this more than adjusting the rotation of the individual elbows, as that may mean that you're not getting them to make the 180° turn you need.

^*I believe this is the same thing isherwood said in his comment.