I have participated in a few high-altitude balloon launches before, and those basically all have a transponder on them, as well. You have to let the FAA know th

I have participated in a few high-altitude balloon launches before, and those basically all have a transponder on them, as well. You have to let the FAA know the time window and get a waiver on the "launch" site, but those can be unpredictable in the atmosphere (some have limited steering of altitude), and you have a (very low) chance of getting somewhere a commercial flight might want to be.