I think a thing to consider is that while the heavier armor makes it slower, it will take less damage when it is getting hit. Perhaps making it near immune to small arms fire, where the other would take damage.
Regardless of how fast the other version is, they both have to come to a stop to pick up people. Even the best pilot in the world is reliant on how quickly people can be loaded onboard. This is going to be several seconds at least of no movement where anyone is free to unload on it.
Not to mention with physicalized damage we may have armor penetration rounds that go through a ship with lower armor, possibly hitting and killing any crew members including the pilot.