So, the balloon flies above 99.5% of the atmosphere, but the telescope hangs under the balloon, so it have to take photos more sideways than straight up? Got to be a lot more than 0.5% of the atmosphere in the frame then.
https://ras.ac.uk/news-and-press/news/superbit-low-cost-ball...
So even if it can't look directly up 90°, it can probably get up to 85° vertical, so it's totally fine.