Just came back today from Mexico, this time from Cancun.
When departing Canada using Flair, I did the online check-in and got my seat number, before going the security area I just passed by Flair line to measure the backpack and put their purple tag. When it was time to board I was holded at the gate for about 20 min while they had to do a lot of checks and manual inputs at computer, I was behind the monitor and I could see all the screens that pops-up.
Three people there had to be involved to clear my boarding , I think they are not very familiar with this.
There are some red warning alerts when they scan the passport , and in 3 spaces they have to get a green tick to allow the passenger to board.
Mine had a red X on timatic part and X in Visa, she had to check in some website if I needed a visa considering my nationality, to board to Mexico, later after entering in some menus, and changing some options, selecting I had a visa, and mine was a Travel document, issued by Canada, she manually changed my true NATIONALITY to XXB.
When I was coming back, I used Westjet, so when I tried to do the check-in online, it didnt allow me. After I put manually the passport information, it showed an error me to conclude it in person. At the desk when I arrived at airport it was faster than Flair, but also took longer than normal.
This time I had the chance to see the tertiary area and had baggage inspection when arriving, since I declared I was bringing dairy.
Conclusion, regardless what you write at online check-in app, they will always manually change things in the computer before allowing you to board.