One more update; it turns out that the fonts weren't getting stripped out in my case. KindleUnpack v0.75 just didn't unpack the MOBI files correctly when used as a droplet. When I ran the script manually on the command line, all the files were there.
The font-family declarations, by contrast, were stripped. Why text-rendering:geometricPrecision would trigger font stripping is beyond me, but I've already concluded that I'll never understand the way the Amazon Kindle folks think....
But now I'm even more baffled why the online Kindle Preview displayed square boxes instead of glyphs afterwards, unless perhaps WebKit's handling of "text-rendering:geometricPrecision" causes the Kindle's built-in fonts to break their font handling code for some reason.