Can't do that because it wouldn't be fair. IMO a Best-of-3 third map should always stay consistent with the first two. I think most would agree.
Best-of-5s are different. If two guys have gone 2-2 after 4 games, we need something to end the competition. It's ok if the balance/faction choices are more lopsided in g5. VP advantage = faction choice on particular map = strong advantage and that's ok. Some would even argue that a g5 should be on the same map as g3 and g4.