Yeah the ik & virtual bones are not handled by IK retargeting. What I did is to implement a new solver that can constraint those bones again. Will publish a video soon about how I did it. So far it supports ik and virtual bones. 
In case you’re interested in learning how I created other tools to make the ALS character intergration more stream lined check out, https://www.youtube.com/playlist?list=PLslFX7TZAr8_kS1zdzEvrjBXI1gMRckZE.
But so far what I lose are the transforms of the ik_hand_gun bone. There I’m still trying to find a solution.