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As a sanity check, I converted again but with font size scaling enabled. ... Suddenly all the generated font-size rules are expressed in ems instead of points, and it looks sensible again.
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My work flow is much like yours, so I have been following and trying to understand the issues you have brought up in two threads. I edit in ePub and then convert to AZW3 for reading.
I always have "Disable Font Size Rescaling" checked in my Calibre "Common Options" dialog. The font sizes always emerge as em units--never pts or anything else. There may be some other issue at work here.