Yes, overlay is the "basic" method- but unless the frames are precisely matching each other, you will see a difference in a number of ways. You need to slowly go from one frame to the other in the overlap region with the appropriate blending method.
Did you ever find a solution? I have exactly the same problem on a 2x2 mosaic. I joined the top two panels, then the bottom two, finally joined the top to the bottom.
There is a “shadow” across the top to bottom join, but none vertically, It matches exactly to the mask generated in PMM, but I don’t see how to use the mask to get rid of it.
I’m not seeing any other parameters that might change this other than Combination Mode, but that doesn’t change the outcome.
An image would help. If the issue is exactly what Bigsos showed, then it is because he used overlay which does not have a gradient of change from one edge to the other using the overlap reason.
Your issue sounds different. A screenshot would be useful here.
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