I will add a 2 cents comments here: never underestimate the Z axis calibration, I had your problems before and was just a matter of calibration on my Z axis (Im a fan of 0.1 and below layers jaja).
Also I will vote a +10 on the overestrusion and here I have something I looked somehow deep: the teeths of the hobbed bolts on the extruders, even the teehts on the bondtech dual geared extruders can have a huge impact on extrusion, to a point where changing them to a smaller size can give you upto 4% difference on the extrusion rate. Even on diferente material you can find a difference: softer material suffer more on this that harder materials. And even speed changes extrusion sice teehts tend to "bite" more deeper if you print faster.