Charles didn't know that yet.
There's stuff he should of know because of what was written in the 60s, and then there was stuff he should have known because it was written much, much later and having a direct on history as it had 'always' happened.
Xavier was unaware of Apocalypse till after his marriage with Lilandra fizzled out, unless i missed some backstory origin, but as far as i remember Apocalypse told Mr. Sinister to make him a perfect mutant host that was not going to rot and burn in the 19th century and then went to sleep till the early 1980s.
Xavier would have had direct dealing with Sinister when acquiring Scott from his first orphanage, and Sinister would have allowed that because he wanted Scott to knock boots with Jean, but Sinister is not a Mutant, and he kept his abilities and agenda on the down low from supposedly the worlds most powerful telepath easily.
Sur was most powerful because of what the Celestial vessel did to him, not his mutant power, so really, anyone that walked into that ship could have been all powerful a day later... But Kang showing up to foster/raise a young Apocalypse lays credence to no one significant before Apocalypse.
What are actually Apocalpse's MUTANT powers? And what's Celestial enhancement?