Hello vicviod,
What do you mean by "trimming photos"?
For alignment you can enable both generic and reference preselection and use keypoint/tiepoint limits that are close to the defaults (40,000 and 4,000 correspondingly).
After alignment I can suggest to run the optimization and then reset region.
In case you are processing some landscape/field areas, you can use Height Field surface type on the Build Mesh step, or even generate DEM from the dense cloud and use it as a source for the orthomosaic generation. Building texture is not necessary for the orthomosaic generation.