Thank you for the feedback, this one took a bit to figure out.
The 1/4" guess is way more than either window actually moves, and therein lies part of the problem, although it's probably within factory spec.
Upon inspection when closing the doors, the glass on the passenger side clears underneath the seal, then pops itself up and nicely into the middle of the seal and is surrounded by the seal on both sides. All good. The driver's side does not clear the seal and sits on the outside, crushing the seal and not sealing properly. Lowering the window allows the glass to clear the seal, so when it's raised it appears it goes into the middle of the seal and seals properly.
Not sure if this is due to window tilt (thanks @OldGuyFla) or the seal being a bit out of position. The good thing is at night the Z is indoors and I leave the windows open 1/16" for ventilation, so the seal is not being crushed continually.
Thanks to everyone for the suggestions, they led me down the correct path.
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