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Nightjar, my understanding is that you want to sell books that can be read on Kindle apps and devices (and on other platforms), but not through the Amazon store. So you are producing EPUBs that the customer can use with send-to-kindle for conversion and delivery. That seems reasonable to me.
You also say that a MOBI produced from your EPUB using Kindle Previewer (Amazon calls this a Master MOBI) will work correctly on Kindle devices when sideloaded. When the user selects Publisher Font then the fonts you added to the book are displayed. But when you use send-to-kindle with the same EPUB the resulting book still shows the Publisher Font option on the Kindle, but does not actually display the included fonts.
In order to diagnose this I suggest that you post an EPUB that demonstrates this problem, either a sample or a public domain book. Then I or others here can follow your procedure and analyze the resulting files produced to see what is different or missing. That may lead to an understanding of what is going wrong and possibly a solution.
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