I noticed the same thing - and I don´t like it, either. It makes no sense from a logical and realistic point of view. It is as flawed as not getting back administrators after disbanding a star base, I think.
There may be a reason for "gameplay" purposes (making the decision of putting troops on a transport more difficult and relevant), b ut - just like the way administrators are never going back to the pool - is at least very confusing to new users (like me!).