I think you can file a NOTAM for a weather balloon even if you don't need clearance. Might depend on the size and payload, though, like if it's closer to a party balloon than a real weather balloon, and how high it's going.
That would explain the difference in experiences. My balloon was 8' diameter at launch and expanded to ~40' when it burst at ~90k'. Mine needed the radar reflector and blinky lights. They were supposed to blink at a certain rate, but we cheated and had lights blinking faster as that's all we could find for our budget/schedule.