I have tested focus stacking with my r5 and the Sony 24-70 GM M2 and the Sigma 105 macro and it works with both. Yes, you have to set the body to manual focus and the lens to auto focus.
I am having another problem with the focus stacking. When I go to the drive mode and set it to focus stacking the screen goes dark so I have to do my front focus first and then set it to focus stacking mode and shoot. I don't know why it's happening but it is annoying as hell. Have to make a call to Sony Pro Services.
I tested my A7RV with my Sigma 105 DG DN macro and FE 16-35 PZ. It seemed to work with both, but I learned that it will take very tiny steps near minimum focus distance on the macro lens, no matter the step setting (even on 10 or wide). It would take 50 shots to move the focus less than an inch, setting on wide. My take so far is that it's not set up for close macro work, it's more for long macro or landscape distance ranges.
If anyone is curious, the focus bracketing feature does NOT work when you use the LA-EA3 adapter with an A-mount lens. Specifically, I was using the SAL1635Z. I tried this the other day and basically the focus bracketing option is grayed out.