Because they have to have different ISBNs anyway, maybe I will make a fonts-embedded EPUB for Nook and other readers that support EPUB, and use the nice one that already works perfectly with EVERY user font on the iPad, for the iPad. I hate to do this, but for this book, it may be necessary.
The font the Nook Color defaults to is Dutch, I believe -- that's what it looks like, when compared to the PD Off option. Times New Roman, if it were present on the device, would probably support the diacritics -- it does on the iPad.
The "including fonts" issue is something we're used to doing in packaging for print anyway. Embedding is not that far away from it.
Thanks, dgatwood and Jellby, for the hand-holding. : )