So, I've been playing around with the latest version of Alegreya that was recently uploaded (
https://github.com/huertatipografica/Alegreya-libre). The new version now contains both Kerning and ligatures.
I was getting fustrated, because the newer version just wasn't being displayed by Nickel or ACCESS properly, compared to the previous version. RMSDK didn't care.
Today, I found out what the problem seems to be. It seems that Nickel and ACCESS do not like having the PANOSE information set in the font file. I set all values to 0 (any), and now there is no wackiness in either the interface (Nickel) or when reading KEPUB's.
So, it seems fonts destined for Kobo Readers should not have any PANOSE information set.