I am late to this discussion, but Micro 4/3 cameras have led the way with focus stacking, in camera. Fuji is playing catch up - which is great to see.
Panasonic and Olympus have been at it for a while, they use two different approaches. The Fuji approach seems much closer to what Olympus does. So videos on the
Olympus focus stacking feature may assist the OP.
Panasonic cameras like the G9 and GH5 have two options for stacking. One is called Post Focus and the other is called Focus Bracketing. Focus Bracketing is similar to what Olympus and Fuji offer. But the Post Focus feature is so fast and powerful I have not used Focus Bracketing.
Post Focus is a two-stage process. After placing the camera in Post Focus mode and pressing the shutter release the camera finds all the focus points in the image and then takes a 6K video of all those focus points. The process takes about 2 seconds after pressing the shutter release. The lens must be in autofocus mode. You can create a focus stacked image in-camera using the G9’s touch screen or use a program like Helicon Focus. Helicon Focus imports the frames from the 6K video and you choose which frames to stack. You get a 18meg jpg in camera or a 50meg (approx.) TIF from Helicon Focus.
The challenges around the Fuji mostly concern DOF issues. A macro DOF calculator or a DOF Table may help. These types of discussions occur over at
Helicon when using the Helicon FB Tube and also in the micro world, see
here.
FF mirrorless cameras are far behind with only Nikon and Phase One offering choices, that I know about. Older Sony cameras can use a very basic focus stacking app (which you must buy) but it does not work with the current A9 or A7 series.
For the last 2 months I have been revising my infield focus stacking technique using Post Focus and working out how to best post process 6K videos. The journey is documented
here.