I’d like to add an additional trick to make sure that the projects you want to merge are located correctly for merging, even if you do not have RTK or GCPs.
You can create MTPs in an overlapping area in your “reference” project, create a .txt file with their coordinates (you can read them at the bottom of the software interface) in the format described in this article: https://support.pix4d.com/hc/en-us/articles/360038397752-Tie-points-GCPs-CPs-import-format-PIX4Dmatic#label3. These can be imported as “fake” GCPs in the other project you want to merge it with (ensuring it’s in the same coordinate reference system). There you can use them to have the project located correctly before merging.
Another trick in case you only need to “align” two point clouds (without the need for having the calibration merged), you can use the “manual registration” workflow in PIX4Dsurvey too.