One could argue why R6 in certain scenarios can be better but like you say A9 is the THE only viable option for professional silent shooting (which seem's to be one of AP's major points for buying A9). Seems to be a hard concept for people to understand.
There were a lot of people complaining that the A9ii was just a minor upgrade on the A9, but it looks like Sony knew what their target market was when they introduced it - and for AP it clearly met their requirements.
I would imagine AP would have got a significant discount over retail prices, simply for the volume of sales - and by switching to Sony as a single supplier of cameras for both video and stills they would have been able to maximize that discount.
As for the R6 - it's too late! AP will have taken months to have evaluated options, etc, and by the time the R6 would have been available even as pre-release samples, the decisions would have already been made, and it would have been down to how much it would cost.