I see a bit of the opposite too.

When I choose Toronto (all airports), the OTAs assume that I want the same Toronto airport for departure and destination. But I don't care if they're different, I live in between and don't drive to the airport.

AC's website is smarter and will readily offer a start at YTZ and return to YYZ.

Aer Lingus still includes luggage on their lowest fare bucket on their own websites, but OTAs only offered web fares at the *same* price without free checked bag. That lost them some business since I wanted to use Expedia points.

Then there was my experience booking a Toronto car rental from within France. The Canadian OTA wanted $200 for the booking. When I went to do the actual booking, I couldn't get onto the .ca site for the life of me. I kept getting redirected to the .fr, but that worked out since it was half price for the same booking. I guess a VPN might pay off...