I had a similar situation. My girlfriend and I took the ferry from Macau to HKIA about a month ago. They requested us to be at the Airport 2 hours prior to flight departure. They still allowed us to board the ferry in Macau realizing that we would only have 1 hour and 20 minutes, without any question. We were flying TG in F to BKK.

The nice thing is that they will refund any already paid departure tax for HKG ^