I guess I could just smash the boards together with six nuts and bolts. That's inelegant but easy. I'd have the screw heads poking out the bottom of the baby board, so I'd have to live with that. I would want low screw head height.
The parts on the baby board will get hot. The baby board pushes against a silicone gap-pad that conducts heat into an aluminum baseplate. Some of the gap-pad material is very compliant, about like chewing gum, so would flow around the screw heads and make a decent thermal interface. I could use thermally conductive putty, but that's messy.
John Larkin Highland Technology, Inc
lunatic fringe electronics ===================================================================
I thought you wanted an air gap between the boards, that's why I suggested two nuts (and it retains the screw and makes assembly easier). You could counterbore the screw head side of the baby board to sink the screw head up to about half the thickness of the board, which would probably make it basically smooth for your gap-pad. Or you could just put a header row of through-hole pins with spacers in the main board with matching holes in the baby board and solder the baby board down. Assembly would be easy, R&R for service not so much :-). If the two boards can touch without shorting, put six pads on the main board and six vias on the baby board large enough to get a soldering iron tip all the way through to touch the main board and solder the baby board down. Like a plug weld, only with solder, and you don't really need to fill the via. Remove with a heat gun to melt all six at once.