Lately many have been stung by making their flight bookings through an OTA only to be redirected by the airline's customer service department, and that led to me wondering what difference, if there are actually any, apart from the obvious price, when booking through an OTA?

I've made many OTA bookings before, and I don't recall a time where I was not given a direct airline PNR, which allowed me to do essentially everything I wanted to, similar to a direct booking. Anyone with back office knowledge who is able to shed some light on this?

Note: tried searching using various search terms both on Google and FT but didn't find anything.