About laser scan reference

This issue os often happening for long narrow objects like roads. There it depends, how you captured the images, what was the flight height and how many lines you used there. The result can be the banana effect. More about it you can find here: https://support.capturingreality.com/hc/en-us/articles/360018811880-Banana-effect-what-to-do-if-my-model-is-bent

In you alignment settings, don’t use image downscale factor set to 3, use 1.

The GCPs should be placed around a whole captured area. There are some places, where are these missing.

Why is there a gap between your captured parts?

Your Camera prior settings is still set to Yes, please, change it to No. On how many images are your GCPs placed?