: I did wonder if skulls might have anything to do with this.

If I had to guess, I would surmise that this is a MCC-exclusive conflict as I've encountered other spawn glitches in my time spent on the game. Nothing as interesting or amazing as this, but I have had moments where entire sections of a map will despawn all enemies. I've seen it happen a couple times on Silent Cartographer between the activating of the Security Console and the Cartographer console where not a single enemy spawns until the batch that appears fighting your way back up. I've also seen Two Betrayals spawn Banshee pilots outside of their banshees as they've fallen to their death and the banshees have been parked and usable (really wish it would do this on Halo so I could use a banshee on a level...) I've done my fair share of glitching and manipulating in the Halo series and I can say there was nothing out of the ordinary about these playthroughs aside from my usual speedrunning.

Never seen anything like this in my time with the game, though. This is quite amazing.