I suspect the retraction settings and or the extruder gear clamping on the filament to be the main issue. I upgraded my ender 3 pro to direct drive for a similar issue. Essentially what happens is that the extrusion goes smoothly when printing long uninterrupted sections, but these under extrusions would appear near or after areas that required a lot of retractions. If your retraction distance is set too small (5-10 mm) the filament gripping gears on the extruder end up going back and forth a lot on the same section of filament in order to start and stop quickly. This wears down the filament itself and suddenly the gears don’t have any traction on the filament to push it, and hence the under extrusion. This is fairly easy to diagnose however. You should check if there is a lot of filament dust around your extruder gears. That was the smoking gun in my instance. I fixed it by reducing the tension in the spring loaded arm and reducing the retraction speed while upping the retraction length to 15mm. I ran with those “fixes” for quite a while before upgrading to a direct drive. Hope this helps.

Kinda weird seeing a reference to a book I just got done listening to. +1 for This is how you lose the wime war.

No no no. You need to take the u-turn at the other end of the universe.