Bear in mind that there's a difference between setting a default body font and forcing a body font.
Setting the default font on the body tag to a custom font shouldn't prevent the device from changing fonts at the user's request, which means Amazon shouldn't have a cow. And if the device is set to use publisher defaults, they'll get the expected rendition for normal paragraphs.
Forcing, by contrast, typically means doing things like specifying the font on individual paragraphs, possibly with !important, and prevents the normal font switching from working, depending on how aggressively you specify the font. You should do that only if the font is critical, e.g. for decorative text like chapter headings. And fonts specified in that way will remain as specified regardless of whether publisher defaults is enabled.
So for your alien text paragraph example, you would need to specify some sort of CSS style class on that paragraph that enables the font in question.
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