I mean what if my only Firebird is up in the air? How do you leave a homedefense squad? With a second firebird? Or do you mean that even if a Firebird is up ferrying troops midway between a base and an alien landing zone, those same troops can defend your base?
No. "Spare soldiers" defend the base.
For example, you hire 10 soldiers, assign 8 to your Firebird, equip them and send to a mission. Your base get attacked, you can equip the remaining two with equipment left on base and fight with them. No need for a second Firebird (or other dropship). If you have more than eight soldiers at base the first eight will be selected (you cannot choose from them ATM).
When I told you soldiers must be assigned to an aircraft to be able to fight, I've been aware about baseattack missions, I didn't lie. It is done via temporary fake-aircraft codewise this case. Of course the plan is to remove this dependency, but it's not an easy job.
-geever