Hello Lampros,
how big differences are there? In which axis?
RealityCapture uses only ellipsoidal heights, so this could be the first part of your problem.
The GCPs are in Greek coordinate system?
Also, what are your alignment settings? Are you considering the RTK precision in the computation? And for such data it is good to know the camera’s calibration parameters. That could help to input them directly into computation.
It is not possible to import MRK file into RealityCapture directly, but you can use the part of it as a flight log. Just create a TXT file with the image names, coordinates and if you want, you can also use precisions (Change the coordinates of the photos - #11 by geoanture86).