As described here https://github.com/MarlinFirmware/Marlin/issues/10812 by @ejtagle (creator of linear advance who seems to quit working on project about 9 months ago) current implementation of linear advance is incompatible with amazing new feature of Marlin S-Curve acceleration.
As far as I understand current (Marlin 2.0.x) implementation of linear advance uses trapezoidal model different from S-Curve Bezier curve profile (see detailed description provided by linear advance author by link above).
I also suspect that direct extruders with low k-factor are more susceptible due to very fast response time. Mine is dual drive BMG extruder with short (~5cm) 1.9 diameter Capricorn tubing going to e3d V6 heatbreak. K-factor is 0.03
If both (LA and SC) are enabled - underextrusion and overextrusion happen at the edges of acceleration/deceleration phases.
Artifacts are especially noticeable with high speed (150 mm/s) and low acceleration (300 mm/s2) - which means longer acceleration/deceleration time and distance and bigger area where trapezoidal model of linear advance conflicts with bezier model of S-Curve.
Attached is a picture with related artifact (speed: 150mm/s acc: 300 mm/s2 k-factor: 0.03). Artifact disappears completely with K-factor = 0 Notice consistent underextrusion at the edge of acceleration/deceleration (where trapeziodal linear-advance conflicts with bezier s-curve)
I use both for a few months and never noticed that. With jerks and junction deviation. My k-factor is around 0.15, direct extruder.
As 0.15 k-factor is typical for bowden - it seems that you have pretty much space for filament bending between exctuder and meltzone. Which alleviates the symptoms.
I have k-factor of 0.03 due to short capricorn (low internal diameter) tube between extruder and meltzone.
If you print at lower speeds (around 60 mm) and with acceleration of 1000 (or higher) - artifacts also should be minimal due to very short and fast acceleration/decelerations periods.
Issue should be most prominent with tight extruder-meltzone space, high speeds and low accelerations.