Hi Isaac,
Nope, I am not working for Agisoft but I am a long-term user of Agisoft Photoscan/Metashape. I am also an official Agisoft reseller and provide training courses on best-practice workflows for digital photogrammetry (using Metashape).
Regarding your question. After importing the dense cloud from CloudCompare into Metashape you are still able to compute a mesh from this shifted dense point cloud in Metashape. You can also generate a DEM from it, but you won't be able to compute a texture or orthophotograph from it because the camera locations haven't shifted and are still at their original locations. However, you could use CloudCompare to generate the orthophotgraph (at the resolution of your dense point cloud) by making use of RASTERIZE.
http://www.cloudcompare.org/doc/wiki/index.php?title=RasterizeThere would be another solution to your problem, but I fear that would include some programming/python scripting.
A) You could use the Open3D package in a custom python script that you run in Metashape to run ICP inside Metashape instead of externally in CloudCompare. Not a quick/simple solution though.
B) Write your own custom Python script that uses the transformation matrix that you get out of CloudCompare when you perform ICP and then apply these values to everything in your Metashape project.
Last but not least (a low tech approach), you could try and generate a mesh from your LAS file which might help you to pick your ground control points better and then use the technique that I explained in my earlier post. Use CloudCompare to generate a mesh from a point cloud. PLUGINS > PoissonRecon.
All the best.
Best regards,
SAV