please add this option to the Missions and type selection:
"Set to transport for ally member, buddies and friends (if Civil ships are within the fleet)"

Hopefully it is possible to detect player inside of the Alliance member list and in the buddy list.
Furthermore the player with a friendly status tag should count for it. (Friends, Friends 2, Wing, Bootcamp)
(if the detection for allies and buddies dont work, then there is still the way to mark those player wih those status tags)

If you have any of them as target, then the mission Transport should be automatically selected, because this is commonly in use for them.
But please make sure, that it should still be on Attack, if only 1 Espionage Probe is selected for the fleet.

optional you can define this behaviour for Civil ships within the fleet and add the following as a suboption:
"Set to ACS defend for ally member, buddies and friends (if Combat ships are within the fleet)"

maybe you can merge this two options into only one single option like it currently is for Espionage (explanation shows the exact behaviour).
so it can be called like this:
"Do not set to Attack for ally member, buddies and friends"

p.s.
the only case where this auto selection doesnt fit is for moonshots, but this is an exception for which the user have to manually change to attack
(moonshots are kinda seldom, so it is ok^^) ...