It's a bit of a side topic to the original but worth some comments.
I agree, mixing combatant levels (personnel, vehicle, etc.) is going to mess things up some, but it should be workable with a little logic.
Not sure MgT applies any scaling rules to hit and damage but that could help. For example, personnel shooting at a vehicle. The vehicle gets a speed DM making it harder to hit, but that should be offset to some degree by the size DM making it easier to hit (both comparative to the personnel scale combat). Though if using the personnel weapons there should be a damage mod penalty meaning while you can hit it you won't do much damage unless you get lucky.
Also as mentioned by DFW one might (should) apply relative speed. So personnel shooting at a speeding air/raft would normally be at a harder to hit speed DM, but if they are also in an air/raft, giving chase at the same speed, it should cancel. And of course they'd have the easier time hitting for the size DM noted above (if such exists, as it should).
And for those BD troopers not having a shot at a fleeing high speed vehicle, sure, IF said BD troopers are plinking away at it with hand held and eye aimed weapons. And IF said BD troopers are just standing there watching it flee. Which of course being BD troopers is unlikely. More likely they'll be chasing with their built in gravbelts and their BD will have enhanced targeting systems and they'll be carrying anti-vehicle weapons linked to it (missiles, lasers, even the FG or PG) all of which will go a long ways to offsetting or negating the speed DM, and then throw in the vehicle size DM for a little more, I'd say running from a platoon of BD troopers is a quick trip to Terminal City.