Thanks to another thread, I was able to find the python command for changing overlay Depth

  gl.shaderadjust('overlayDepth', x)

where x is overlayDepth.

As far as I can see, the default for overlayDepth is 0.1, but I'm not sure what the units are. thanks

It would be really helpful also to have this covered in the python commands on Github. It mentions shaderadjust, but it's not easy to see what commands are covered, and an example of the various things that can be adjusted would be very helpful.

The overlay depth influences how well you can see an overlay image hidden underneath the cortex. The value ranges from 0 (cortex is opaque) to 1 (crotex is transparent at locations where there is subcortical activation). Usually values around 0.2-0.4 do a nice job of revealing the subcortical activity translucently to also show the cortex. You can interactively adjust the 'Overlay depth' slider to see this effect, as shown in the attached image: