If I build a Rebel Transport worth, say, 60 points will those 20 points (in excess of the 40 for RT + Combat Retrofit) cut into the amount I get when choosing my force for the missions. For example, would that leave me with 105 squad points in the first mission?

Depends. Some of the missions state how many points that the transport can use, and that is outside of the normal squad building points. But in general terms, unless the mission specifically tells you differently, all upgrade points count towards your squad point total.