I just noticed that when I hit the transport button on construction AGO will still use deploy by default if I have "deploy on own coordinates" set. This behaved differently before the change of fleet 1. It used to use transport when called from the constructions list.
I guess the transport routine should use the transport mission?

Sorry I couldn't be with you guys for the meeting. I don't think you need to change this back anyway, I used deploy to send resources for projects on planets with moons and jumpgates often anyway.