They can if the BRF are a marjoity share holder.
But more likely they ask as a simple curtesy. I am sure Qantas would bend over backwards to comply with a request by the palace.
It could also be that as the RF don't often use Air Canada KP simply were stating what they usual do for other members of the RF when they fly. With some exceptions (Harry has used Easyjet and the Cambridges have used Flybe) the RF seem to use British Airways who are therefore probably well rehearsed in what the expectations for royal customers is. I don't see the issue with simply stating some ground rules to follow, more likely Air Canada asked what was expected and KP replied. Of course they would say they don't want photos taken all the time and people coming up to her, it doesn't mean Meghan is going full on "don't look even look at me" diva.