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I have confirmed it, using the false exit and repeating the tunnel to Miracola section, will reduce the number of points you get. This also applies to the graveyard level, which also has false exits. I still have not confirmed if the same rule applies to repeatable battles in Zoda's Revenge.
I did my best to minimize the number of enemies killed, even walking through some (the Slug in the graveyard level) to minimize the number of kills. The first section of Chapter 7 can be a little more problematic with those pink guys on those hover bikes. It's almost impossible to survive chapter 8; since it's one narrow pathway, you WILL take a lot of damage from the green/brown aliens if you avoid killing them.
By the start of Chapter 8 I had 83550 points. 90840 after completing it, but since there are constant respawning enemies for the last two bosses (brown aliens when fighting the spaceship's core, little crawling aliens when fighting Zoda) I'm pretty sure this isn't the highest possible score. It's almost impossible to survive these battles without killing those respawning enemies.
"If drumsticks are for playing drums, you'd think breadsticks would be for playing bread, wouldn't you?" ~George Carlin