Halo Jakub,
it seems that the polygon export from qGis using S-JTSK / Krovak East North produces Coordinates out of range.....
I would add your point cloud into Metashape (first setting the chunk CS using EPSG code 5514), create the outer boundary and then export specifying the CS and checking the correct toWGS84 parameters as there up to 5 different sets of parameters... see following
PS. I think I found why qGis and possibly DJI Terra export coordinates out of range. It seems it uses AUTHORITY["EPSG","102067"] which is different from 5514 (XY rotated and X inversed):
PROJCS["S-JTSK_Krovak_East_North",
GEOGCS["GCS_S_JTSK",
DATUM["D_S_JTSK",
SPHEROID["Bessel_1841",6377397.155,299.1528128]],
PRIMEM["Greenwich",0],
UNIT["Degree",0.017453292519943295]],
PROJECTION["Krovak"],
PARAMETER["False_Easting",0],
PARAMETER["False_Northing",0],
PARAMETER["Pseudo_Standard_Parallel_1",78.5],
PARAMETER["Scale_Factor",0.9999],
PARAMETER["Azimuth",30.28813975277778],
PARAMETER["Longitude_Of_Center",24.83333333333333],
PARAMETER["Latitude_Of_Center",49.5],
PARAMETER["X_Scale",-1],
PARAMETER["Y_Scale",1],
PARAMETER["XY_Plane_Rotation",90],
UNIT["Meter",1],
AUTHORITY["EPSG","102067"]]