My questions are does the prototype shop on mission 7 have to be a tie interceptor or can it be another type that is not a named pilot. The second question is does the ability of the facilities carry on or do they only take effect when touching the facility. Thank you

Obviously the scenario was written with the interceptor in mind, but It can be any kind of ship. Decimator might be interesting.

Once activated, the buff stay until the relevant facility is destroyed.

Most of the missions are designed to be customised a little. It's generally encouraged to try different options in order to get used to the ships and their various nuances.