Deeply rooted skip?
If you could somehow prepare or activate either the "WaspsNest_Elevator_BP" or "WaspsNest_Beetle_BP" level early, you could skip the boat and darkroom sections.
If this level was somehow loaded early, you could get any of the "Elevator" checkpoints, the "Beetle" checkpoint or get the Minigame "Plunger Dunger" and MGW to it to continue progress. Fastest in this case would be the "Beetle" checkpoint.
To the best of our knowledge there's no way to prepare this level outside of finishing darkroom. The level is loaded into memory the moment you're about to land on the flying fish in darkroom.
Skipping all the way to Extermination doesn't seem possible. That would require the "WaspQueenBoss_P" level to be loaded into memory, which happens when you get the "Beetle Ride" checkpoint, and you would need the beetle itself to transfer into Extermination. Maybe it's possible to get the beetle OOB and skip part of the beetle ride?