Not sure what you mean about the names not being important, please clarify. I need to match the names to update the coordinates from the GCP file. (That's a minor issue, as you can edit the GCP csv to match the labels, i.e. "point 1".)
In the import reference dialogue there is a checkbox that "ignore labels", try it and you will understand. Metashape manages to match markers and ground points on its own (obviously it can fail if points distribution is too much regular making several matches plausible)
Also you may need to see if by enabling "refine markers" under tools menu, you get the boost you want for your workflow. (also needs some user care, that is why it is not enabled by default)
Best regards,
José Martínez
Geobit & Accupixel
Metashape traning