I can confirm the discrepancy with the font handling. I use "Palatine" for e-reading on my Touch (will provide the .ttf for testing if required).
Under a kepub, Palatine displays and behaves fine.
Under a epub, the hinting disappears completely and the font is unreadable.
The irony is that the font appears perfectly fine when displayed in the font selection drop down on the epub. The problem occurs once its selected and applied.
There also appears to be some discrepancy with the application of stock fonts as well between kobo epubs and regular epubs. I've tried this with a range of epubs from various sources.
I've a feeling this will have something to do with the style formatting in the kobo epubs and its interaction with the new font-rendering, but I've not got a whole lot to go on bar my gut.
If anyone from Kobo wants more details and information, I'm happy to be contacted via Twitter (kianryan).