From what I can gather, the roof the shooter was on has a slight incline towards the shooter’s head. It is possible that the counter-snipers couldn’t see him because he was below their line of vision until he raised his head to take the shot.
New info: Sources are reporting that a local law enforcement officer encountered the gunman who opened fire at Donald Trump’s Pennsylvania rally just moments before he fired at the former president.
https://youtu.be/NP86CksBmoU?si=n4-heC1k4L9BbE1r