Offizieller Kommentar
We recommend using the normal workflow you have been using and then using GIS software to do the final GPS coordinate adjustment to get more precision. Our manual GCP workflows are only designed to be used with non-geotagging cameras and won't actually lead to higher accuracy.
You can read about getting highly accurate georeferencing our our outputs here:
https://support.dronesmadeeasy.com/hc/en-us/articles/115003655066-Georeferencing-Aerial-Maps
If you really want to fix your manual georeferenced layers, here are the support articles regarding this issues you are seeing.
https://support.dronesmadeeasy.com/hc/en-us/articles/207959283-Map-is-rotated-strangely
https://support.dronesmadeeasy.com/hc/en-us/articles/207667206-Map-is-scaled-incorrectly