Hi Kieren, I tested this carefully on WIndows 10, with lilypond 2.19.82, and Alegreya Medium from Huerta Tipografica direct. All works fine. The output PDF according to Acrobat Pro DC shows two fonts from your example, Alegreya-Medium (Embedded Subset) and TeXGyreSchola-Regular (Embedded Subset), precisely as expected.
Yet my pristine mac install shows issues. I don't believe this is a local problem with your computer. Will report back. Andrew
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