The speciality produce in this mod requires items above or below a hive, ex: wither skulls on the hive, diamond block below.

Does this work with alviary? I can't produce specialities from an alviary at all.

After moving TNT to under the alviary apocalypric bees seem to produce the specialities, so that's all good for those bees that require items beneath the hive.

However I can not get withering or wither bees to produce skulls/star fragments by placing wither skulls on top of the alviary.

I'll say that is a unintentional "balance" feature.