So the problem has finally been resolved! The problem was a gummed-up or non-smooth spinning extruder gear, specifically the grey tensioning/pressure one. I thought I found this earlier but there was very strange behavior. When I first took apart the extruder many weeks ago, the tensioning gear didn’t spin smoothly, but when I reassembled the extruder assembly, it spun perfectly for some reason.
Additionally, the problem seemed to go away when printing with my BBL Red Matte PLA, so I thought it would be the filament. Perhaps I just overlooked the imperfections in the red test prints. For these reasons, I ruled out the extruder gears for the time being. Eventually, I made it back to the extruder gears as the support team thought it could be a bad extruder motor, and low and behold, the grey tensioning gear was still gummed up, and when I reassembled the extruder gears, the problem persisteded (unlike before). I tried putting some WD-40 on it to get it moving again, but it didn’t fully resolve the problem. The support team sent over a replacement set of extruder gears, and it now extrudes nearly perfectly again!
There is still slight under-extrusion with my test print, but this is a large flat object, so I would expect to have to increase the flow slightly and tune the pressure advance more carefully to get perfect results.
Problem: Seized/Rough/Dirty Extruder Gear Bearing (Specifically Grey Tensioning Arm) causing inconsistent underextrusion.
Solution: Replace Extruder Gears.