Hey Andreg,
If you are going to have 11 chunks, they need to be treated as separate projects so I would do 10 markers/ GCP's for each chunk. (You could probably get away with 6-7 per chunk). I am not sure about the orthophoto since I have never exported an orthophoto before however for the orthomosaics I would use High Alignment (preferably), if not Medium Alignment. Moreover you can either generate them using the DEM, Mesh, Sparse Cloud or a Dense Cloud. I would use the DEM as my first option. However the advantage of using Mesh over DEM is that sometimes DEM is not generated accurately and if you are creating your orthophoto or your orthomosaic based on Mesh, your orthomosaic wouldn't be affected even if your DEM is not accurate.