This may be something I'm just missing, but it seems by a strict reading, the Incantatrix (I also checked the Mystic Theurge, I'm assuming some of the other prestige classes), no longer get the two free spells per level known added to their spellbook. Is this the case? Would those fall under 'other benefits of that (base) class?'
An incantatrix continues to study standard magic as well as pursuing studies in metamagic. Thus, when a new incantatrix level is gained, the character gains new spells per day as if she had also gained a level in a spellcasting class she belonged to before becoming an incantatrix. She does not, however, gain any other benefit a character of that class would have gained (bonus metamagic or item creation feats, for example).