If it was something like £60 with lastminute vs £80 with BA, London to Jersey in 3 weeks time, where there's a 99.9% chance of me taking the flight as booked, I would be happy to book with the OTA.
An expensive fare for a multi-flight itinerary far in the future where there's a more than minuscule chance I might not be able to travel or that BA might cancel or significantly reschedule some flights, are factors that would be against me booking with the OTA.