I waited to reply to see if anyone had any specific answers to your problem. I don't have an ATEM anymore, but I did when I started using vMix about a year ago. What you want to do may be possible, But I don't know about the logistics of using 1 controller to control 2 pieces of software.

What I can tell you however, is how much of a pain it was to try to get the 2 to work together. I can understand what you want to do and hope you can get it to work because it will solve a problem that I have dealt with in the past. But, I have since sold my ATEM and purchased additional input cards so I can bring my video straight from my sources to vMix. I now use the Tally Light feature built in to the web controller, which was something I couldn't utilize while using the ATEM either.

I fought removing the ATEM from my production setup since I had been using it so long, but I have never looked back after selling it and using vMix to switch my sources.

Just my 2 cents, I'm not trying to sway you in one direction over the other, but I feel your pain. It was very tricky trying to coordinate the dance between my vMix setup and my ATEM switcher operator.

Good luck
Chuck