I have some sort of conclusion.
The pixel jump is only isolated to this one particular project.
It’s not a Mocha issue as far as I can tell but an After Effects issue.
I tried to replicate the issue with different file types and workflows but it only appears in my current project…and it’s due to Adobe Link. While using Premiere, I selected the file and chose Replace with AE Composition via Adobe Link.
In that comp I duplicated the .mts and stacked it.
This time I added an AE mask, and the image jumped up exactly one pixel.
I deleted the mask and the layer returned to normal. The transform values did not change, it was only a visual change that you can notice when you toggle the layer opacity on and off.
I’ll probably submit this to Adobe.
As far as my current projects goes, before I found the issued I ended up adding a ‘refine matte’ effect and then roto’d out some pixels to where it looked good.