Are these RTK coordinates implemented to the images? What are your alignment settings? Do you consider the achieved precisions of the images in your process?
Yes, it is basically a normal process for such situation. Just try to capture the images in similar conditions (like cloudy one).
There is no image limitation. The only limitation is your HW. If the number of the images is over the RAM limitation, you can set the lower number for detected features in the alignment settings.