Colliding fasteners in electronics retrofit project

From the comments:

The countersunk screw from beneath is a no-go, unfortunately. There's an assembly paradox here as well, the adaptor has to be installed before the new PCIe device can be attached to it. If the screw head is underneath then you can't get a screwdriver in there.

We're not beaten yet!

enter image description here

Figure 1. Insert countersink screw from below and add a locknut to leave a male "stud" sticking up from the orange board. A dab of super-glue might help.

  • The orange board can now be installed first.
  • The blue module positioned and a nut and optional washer added to the top. If there is a risk of over-flexing the top unit then add a space between the lock-nut and the blue board.

Another thing you might explore is "binder screws." They have a very thin, flat head that, secured with a little superglue, could solve your clearance problem and make disassembly easier to boot: enter image description here