You've got a point, and in fact that brings up another question; Why do they all want to save him? All of them, even the armor, want to rescue this man, possibly invalidating my suspicions. BUT! Remember that Khonnir is a wizard, and wizards can cast enchantment spells. What spells could a low-level wizard use to cover his tracks? Charm Person, Hypnotism, Memory Lapse, Sleep, ALL of which are level 1 wizard spells. He could do as he pleased, and either they wouldn't resist, or they wouldn't remember anything that happened.
Worse yet, if this is the case, we could even theorize that he's responsible for the kobold's choice of attire. She's exotic, small, normally acts smug and arrogant; The perfect toy for a depraved wizard to break. He uses magical suggestions to make her dress like a slut, let her flaunt her stuff and turn her nose up at others. And then, when she's under his spell, he takes her back to his Back Room and ravages her, breaking her and then ensuring that she never remembers it, just so he can do it all again.
The halfling, and his motivation to save his real father. What's been keeping him in Torch for so long if he's been meaning to get out and stage a rescue? Perhaps the wizard has been using his spells to persuade him otherwise, and lure him into the Back Room again. And for that matter, who's the machine that saved him in the first place, and why would she just leave him in front of Torch, why Torch specifically? Well I only know one person in Torch who knows how machine's work, and that would be Khonnir Baine!
But we don't know just when this horrible person strikes. Does he get them while they're young, or groom them into his little pets once they're grown? Is Connall, his gay lover, in on this whole thing, or has Khonnir been hiding it from him all along? Why does the AP give us almost no information on her? Someone, get me non-spoiler information on this girl, stat!