Pitfalls of flying on separate tickets

Since our connecting flight will come from Canada, not the EU, will
they make us go through customs in Athens before boarding our flight
to Santorini on a different ticket?

Yes.

I'd check FlightAware and research the dependability of your intended flight. My last two international flights had significant delays- one 24 hrs and one 6 hrs. Where would that put you? I have decided to always give myself an extra day before transiting to another city after arrival.
In any case, have a great trip.

You would go through immigration in Athens either way.

If you are checking luggage, you would check your bags through to Santorini if on one ticket. If two tickets, you would have to claim your bags in Athens and the check them in for your flight to Santorini.

If you are on separate tickets and your Air Canada flight is late and you miss the Sky Express flight, you will have to buy a new ticket at that day's rate.

Your Athens-Santorini flight must in any case and as a precaution allow you a layover in Athens of at least 2h30.

So, on June 24 morning, if your Air Canada flight arrives at 9.40am, the 11.10am Aegean flight to Santorini would have been too early anyway.

With Aegean you could take the next flight at 1:30 p.m. It is true that it costs around 50€ more than Sky Express flights, but not hundreds of dollars

Have you looked into flying from Seattle to Santorini on one ticket? You would obviously have a layover somewhere. By traveling on one ticket, if you miss your flight to Santorini, the airline is responsible for putting you on the next flight to Santorini. And you don't have to worry about your luggage until you arrive in Santorini. Last May we flew from Boston to Santorini with a layover in Zurich on Swissair. it was so easy.

Stephanie, where are you looking up flights? According to Google Flights the difference in airfare between Seattle-Athens RT and a multi-city flight Seattle to Santorini and return Athens to Seattle is about $100. I don't see any significant cost savings doing it with the separate tickets.

Thanks for the advice everyone. It is the clear the advantages of booking on one ticket far outweigh the increased cost. So that is what we did!

@ Stephanie. Thanks for coming back and sharing. I hope you have a wonderful trip.