Hello Sarbian,
I believe that, while using landing guidance through an atmosphere, you are simulating an object falling prograde rather than retrograde.
I tested this against Trajectories, which is very accurate, and it's prograde setting lines up closely with you decent line.
Mechjeb has been inaccurate for over a year for landings that are very shallow through an atmosphere.
MechJeb can fly anything with the right attitude settings.