The health gating is to allow for a comeback. Killing enemy guardians while invading will regen boss health. Killing waves of primevals will give an increasing damage buff against the boss. This buff after a number of waves will let you just melt the boss and win.
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I know all that but sometimes it seems like the team on the comeback end, has less damage phases and can just nuke their boss. I've been on both ends and even when it happens in my favor I'm just like "oh. The game is gonna let us just melt our boss? Oh. It's over. Wow lol."
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As far as I'm away those are the only mechanics. It's possible the comeback team just did a better job at killing the primeval.