Indeed. During IRROPS you are under airport control and I has no issues the two times this happened despite is being a OTA booking.

Where some people appear to have had problems is pre travel and there has been a schedule change for example and it can take a little more work to get alternative flights booked. From the complaints I read on various threads on here some of those people are also unreasonable in their requests for alternatives and even if booking direct the airline would turn them down.