This is the most likely reason, IMO. I would think that changes in the supplier or the supplier's manufacturing methods over time accounts for most of these variances.
Dials are a completely separate animal. The inner bezel was/is typically sold with the crystal so you could have an original bezel with a redial, or you could have an original dial with a fake or aftermarket bezel. They need to be assessed independently.
This is really interesting stuff! I own a Yachting (see below) and I too fuss over the minutiae but I've only ever noticed the alignment of "TACHY".
Two things I'd suggest adding to the 8 specimens you've already documented. One, check ebay, I believe there are two sellers that carry service/replacement replacement crystals/bezels. Those could help separate what was the norm for the period vs. what is common on the service parts. Two, do an image search for "Tissot Navigator Yacht". Those were powered by the sister movement Lemania 1341 and had very similar cases and what I had until this post assumed were identical bezels.
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