Chris,
Thanks for your interest in this feature. The pocket screw hardware pattern is fixed and cannot be changed. To switch face sides for the pocket screw, simply go to construction parameters for the part in question and select the side you want them on (it can be different for each part and each edge per part). You can also decide per edge if you want the mating part spot holes (I’ll explain a bit later).
The challenge for this joinery was efficiently fabricating special angled pocket-screw holes using a standard, 3-axis CNC machine, without the need for specialized drilling heads or tooling, and without the need to remove/handle the part for additional discrete operations.
The following drawing gives an idea of what the result at the Thermwood machine will look like when ran through Control Nesting (In eCabinet Systems, it will look boxier).

We use a 3/8” flat router bit to create the main angled pocket hole. This tool ramps down at an angle and then drops to create needed clearance for the screw head and then ramps out to create a perpendicular wall to the main ramp in move. As an option before this main pocket machining is performed, we can take a 1/8” or up to 5mm flat router bit and plunge a hole to create a ledge in the screw head surface. This ledge is used to locate the tip of the screw and guide it at the correct angle. After the ledge hole cut, there is yet another option to use the same tool to create a clean-up along the two outer edges of the screw head surface to create a flatter surface for the screw head. This clean up pass may not always be necessary, however it proved to be helpful in preventing cracking/splitting of melamine or pre-finished material surfaces. If this is not a concern, it can be left out. The screw tip ledge has proven to be very useful for guiding the screw at the correct angle. The result will looks similar to the drawing above. This method does not have a pilot hole through the part, so a self-drilling screw is recommended and seems to perform well. The following cut away view shows more detail on how this works.

The head of the screw lays on the main curved ramped in surface and the tip sits in the ledge thus aligning the screw to the proper angle. Now, you attach your driver bit and let the self-drilling action of the screw lead it through.
Another component of this joinery is an optional shallow spot hole that is created on the mating part. This option is defined in eCabinet Systems and can be turned on/off per part edge. See picture below (picture shows lock dada with pocket screw).
This spot hole serves two main purposes. First, it clears any hard melamine, laminate, or pre-finished surface that tends to prevents the screw tip from easily getting started into the mating part. Second, it helps minimize the chance of the material surface chipping and bulging up hindering a tight connection and also helps provide a relief for any bulge out from the screw exiting/entering the connecting parts.
Hope this helps explain the joinery a little better and thanks again for your interest.
(Machine user note: Only supported in Control Nesting version 5.78 or newer. Please refer to Control Nesting manual for tooling setup requirements.)