I don't know which transit you mean.
Check-in is regular if you have filled in all the right documents and had your tests or vaccinations. When you haven't you will be requested to do so first and come back later.
Customs was also regular. No waiting time when we went ( in the evening)
Yes, make sure you have the right documents. Athens airport was pretty packed because few people didn't have documents and there was a hold up in checking to see if the everything was in order. I haven't been to Santorini this year though so I can't tell you for sure
I can't say enough about how much I loved visiting cape columbo! I love unorganized beaches because im so sick of the music they play at these beaches, I want some peace and quiet! And the water is super warm which is great for the off season. Have any of you been? What did you think?