Hello Vadim,
There's importCameras() function that allows to load the EO/IO data for the images, thus allowing to skip alignCameras stage, however, it is still required to match images, if you are interested in generating depth maps, dense cloud, mesh after importing the cameras.
So workflow in this case would be:
addPhotos
matchPhotos
importCameras
buildPoints
The latter two substitutes alignCameras operation assumed by common workflow.
Instead of using Import Cameras operation, for example, if you have some custom date format, you can "manually" using Python form the 4x4 transformation matrix for each camera according to it's location and orientation and load the calibration information to the corresponding sensor instances. Then match photos and build points.
Import Reference does not substitute alignment / import cameras, it just loads the reference information for cameras and markers to be used for the model referencing. However, you can use this data to form mentioned transformation matrices.