I'm just tossing this out there "ortho". So don't shoot me. I see that your vertical alignment is right on the money. But don't see anything for horizontal. (Maybe just too faint to see???) Which of course will account for the positioning of the cowl to the motor. Question? Does the cowl fit the rest of the fuse nicely? As in, straight and true? With the exact horizontal plane going straight through the fuse, where is it in association with the horizontal alignment of the motor? My guess...and it is only a guess. If the motor is not true with the horizontal line through the fuse, you may find by aligning it so that it is, the plane may even fly better than it does now. Find your fuse incidence and adjust your motor accordingly. That is what I would do. Again, just a thought I am tossing out there.
Was it aligned before the down thrust? 1 or even .5° can make the difference.
Thrust and datum lines arent really adjustable to an airframe I believe, im no engineer, what I know about those things I read from the incidence meters manuals and glo kit plans but we have the benefit of mixes to correct all the habits that might show up.
im thinking a few mm wont make a big difference in overall flight that cant be corrected.
Id really like to know the technical answer though, rc specific not full scale wise. Interesting subject.