Brill has published a font family for its publications. I admit I haven't looked closely at its legal limitations, but anyway, it's a nice step in the right direction: it has full support of Egyptian translitteration, including "Egyptological yod", made with i and U+0486 (as expected, the alternative with U+0313 places the accent above the "I", and not in front of it - this is indeed normal for a general purpose font).
The only problem is that the "lowercase" Aleph is too small. In fact, lower and upper case aleph should have the same size. But, anyway... well, the other "only" problem is that many softwares don't get it right. I'm still disappointed that mellel, which is supposed to be very good at font handling, misses the mark here.
You can find the font here : http://www.brill.com/author-gateway/brill-fonts
P.S. After a look at the font use conditions, non-commercial uses are allowed, such as "embed the document in a pdf or the like which is published on Licensee's website". Commercial uses are not, so for instance, it can only be used in books published by Brill.