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octomap_server which you used for mapping does not reason about height or inclination in any way of the incoming data. It will just use a tf lookup from your sensor's tf frame to the map frame in order to align (register) the scan in the world frame.

This information has to be provided by the user, in your case it's coming from RGBD-Slam. Already there, your data must be tilted. I would assume that it will be better if your camera is aligned horizontally for most images, particularly the first. Adding an IMU and integrating it will completely solve this problem.