I think HE'S more likely Ahsoka's archenemy.
We might get a reason soon. Palpatine's eyes and ears are not perfect. It could be an encounter or a vision. That really just depends.
I am also pretty sure a few Inquisitors knew, like the Grand one. Keeping someone's identity hidden is not always foolproof. Maybe we might learn that Skoll was at the Jedi Temple during the sacking and saw Anakin. Then he encountered him as Vader somewhere. Both encounters playing a role in his fall.
Saying Palpatine made sure no one knew Vader's true identity is like saying Order 66 was foolproof. Besides, Thrawn and Tarkin knew.
How exactly? Injuring Sabine doesn't count, as Ahsoka arrived in time to give Sabine the treatment she needed. Skoll accused Ahsoka of abaondoning Anakin, which brought back Ahsoka's memory of that vision on Lothal. She may have kept a pokerface, but it did effect her on the inside. She was able to recover after her lesson with Anakin on the WBW however. There might be more in the next season. Skoll is likely going to be more dangerous than Morgan too.
But he did strike her on an emotional level, something Morgan has NOT done.
That history was not expanded on that much. Besides, Mando season 2 feels like they just met. Baylon is more familiar with Ahsoka, as he is with Anakin. Baylon did use his words to bring Ahsoka down a peg in their first fight.
I think HE'S more likely Ahsoka's archenemy.