Possibly something like this exists already and I haven't noticed it. If so, sorry to have wasted your time.
Anyway, I was thinking that when placing groups (specifically groups with vehicles) in the editor, a 'Special' field should appear (as it does when placing individual units), which should give the option as to whether the infantry in the group should be spawned inside or outside their vehicles. I know this can be achieved by editing each unit separately, but this takes time (not much, I know) and gets tedious (or maybe I'm just impatient) when doing so for large amounts of units.