Output coordinate system is not the same warning on merge

I have 13 flights (at least) of a 1,000 acres that I need to merge. I am getting warnings about coordinate system mismatch, but I double checked and they are all identical. The only thing that is slightly different is the geoid separation, but it's very close, less than a 0.1' difference across the site. Landing areas differ and I based my geiod heights on the UAV location at each flight. Must all geoid separations be identical or does the cause of the error lie elsewhere? GCPs are not used. All data is based on eBee RTK info and projects created via emotion 3.

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