Why would an email have much lower open rates in the final part of an A/B test, but only in Gmail?
It's the metric. Open rate is not a reliable metric. An open is tracked through an image pulled from your crm server. If images aren't loaded the open doesn't get recorded. Further, Gmail uses something called image image proxying, i.e. they cache the images on their servers instead of pulling the images from your server.
Click rate is a reliable metric, though, so maybe construct decision making around that?
In any case it is still possible your emails are ending up in spam. There are services like glockapps that can help you figure out if this is the case.