New to my ST, and new to the forums, but I will say that I've done some extensive work on Ford IRS suspensions with my 2016 Shelby GT350, and one of the modifications I made to it recently might be a benefit to the "three-holer" ST owners. Here's a writeup I did about some improvements I made on my GT350:
https://www.mustang6g.com/forums/threads/4-56-gears-and-qa1-carbon-fiber-driveshaft.174916/
About midway down that writeup, you can see the larger bolts I used in all four differential mounts. I haven't yet been under my new-to-me 2020 ST (which I assume does have the four-bolt setup), but I suspect that like the S550 Mustangs, the differential cover could be drilled and tapped for a larger bolt than what Ford used from the factory.
I'll dig into this deeper the first time I put my ST on the lift, but this might be something to consider for the three-bolt setup.