My greatest fear is lack of control and benefits
I recently booked a flight with opodo because it was cheaper than the BA site. I then realised if you wanted to do exec club based things, like upgrade with avios it was very difficult. Luckily BA rep helped me out and managed to do it 'manually'
I too would like to know what 'rights' you officially lose because you book through a TA ; does BA in effect 'wash its hands' of booking management