This photo from an answer on the Shuttle Approach and Landing Tests shows the front attachment between the Enterprise orbiter and the Shuttle Carrier Aircraft. The support strut reaches the attachment point through the opened landing gear doors. The landing gear is also lowered.
During the ALTs, between the aircraft separation and landing, was there a period of time when the landing gear were raised and the doors closed? Or were the landing gear just left down and the doors open for the entire glide?
It's my understanding that Enterprise had no hydraulic system, so I'm not even sure how one would even do that. On the other hand, it would seem that it would make a difference in the Enterprise's flight response.