As I mentioned in the private message, there are a few factors you need to take into consideration:
- When you process imagery that has very precise RTK geotags, you need to ensure that you have adjusted the accuracy associated with your images in the Image Properties Editor. If there are no GCPs in the project, the absolute geolocation is taken from the image coordinates. The software needs to know how much to trust these coordinates, this is why setting the correct accuracy is important. When using RTK technology, the image accuracy should be much better (few centimeters).
By default, Pix4D assigns to your images a 5-meter accuracy in the X and Y direction and 10-meter accuracy in the Z direction. Make sure to appropriately adjust the accuracy associated with your imagery before processing. You can read more about changing your image geotag accuracy in our article https://support.pix4d.com/hc/en-us/articles/202560019-How-to-select-change-the-images-geolocation-and-orientation
The accuracy of the image geolocation is read from the EXIF file of each image and it sets the weight with which each coordinates will be taken into account for processing. In case you doubt about the accuracy of your system, the best way to find it out is to check the specification or to consult your GPS manufacturer.
What is the coordinate system in which the images were acquired and what is the coordinate system in which you want to have the outputs? If the images were acquired in WGS 84 (horizontal and vertical), the vertical coordinate system of the images is incorrectly defined as EGM2008, so we recommend you set it as default (WGS 84 ellipsoid).
You can resolve the high internal camera optimization by setting internal optimization to All Prior. This will keep the optimized values relatively close to the initial values from the database.
We still recommend that you use GCPs with your RTK system. Your RTK system may limit the amount of GCPs you need to use in a project, but GCPs are still essential to incorporating a high level of accuracy into your project. Read our article Do RTK/PPK drones give you better results than GCPs? which compares an RTK project with no GCPs with a project with GCPs.
Let me know if this helps.