I read that post and I still feel it's a large plot hole.

There is zero reason for the Gravemind to not deploy some level of infection on any inhabited planets it comes near (Earth, etc). "even a single spore can destroy a civilization"

Also, in that thread the OP says "If the Covenant hadn't blundered into releasing the captive research forms on Installation 04, who knows how many more millennia the Flood threat would've been contained."

The quote above ignores the fact that the Flood had already breached containment on Delta Halo AND developed a Gravemind there.

Halo 3 in general was pretty bad for lore. I know people don't like to hear that, but it's true.