The simple answer is no, there is no option for changing take off points in general. However, on 3 of the pacific maps (Kyushu, New Guinea and Okinawa) it is possible to toggle army occupation between bases, which in affect enables a variation off take off points. Have a browse through the help file where this is explained in more detail.
I have considered making more than one airbase available for each army with each map, but it would mean a considerable increase in work for each new map, which I don't believe is justified considering the scope of Mission Mate.
Thanks for posting.