I just checked, and Boris got the full run-down on the actual situation with Agatha vs The Other. Today's comic indicates that he has passed this information on to the Baron, and I expect the Baron is smart enough to figure out just how much this explains the dynamics behind events in Sturmhalten and especially his Wasping and the aftermath - Agatha's sudden change when she put on the necklace.

I think the Baron may be running a multi-layered plan with fallbacks, here, designed around the conclusion that Boris's information is completely correct.
A) Agatha is the greatest potential threat to Clankrezia in existence. Therefore, give her as much room to strengthen her position in preparation for that conflict as he can get away with.
B) When he is inevitably forced to take action against her, leave her the opportunity to escape and resume fighting even if he does initially beat her.
C) If the two of them come face to face and she knows about the Baron being wasped, from any combination of deductions, memories stolen from Lucragatha, Tarvek, or the Baron himself giving her information, she may be able to countermand Clankrezia's orders. Capturing her alive may make such a meeting possible, and if he can pull it off it would be an instant coup against Clankrezia and drastically change the conflict.