This same problem came up quite recently when someone was trying to get Amazon's Ember font working correctly on a Kobo (both epubs and kepubs).
I did a step-by-step on how to fix this kind of problem. I used Ember as the example but you can fix Bookerly in the same way
if you have the time and inclination. The
original thread is here, posts #2 and #9.
Someone also consolidated the details to
the Wiki if you prefer to read it there.