I’m not following the question. What setting are you looking to change and why?
Note that there are 2 discrete calibration activities: lens calibration, and camera alignment. Lens calibration does not depend on any specific size of bed. Camera alignment will need to be done with the post lens calibrated camera being rigidly mounted and in full view of the laser work area.
No. You needn’t remove the honeycomb. However, keep in mind that the camera alignment is really only precise at one focal distance from material to camera.
So I’d suggest putting whatever you would have at typical burning heights for your needs.