Jay,
There are basically 4 approaches that you can take regarding the hinges:
1. Build the sides all flush with the edge of the face frame
2. Block out the sides flush with the face frames at the hinge locations
3. Use a hinge and mounting plate where the mounting plate fastens to the back side of the face frame
4. Use the Salice program of mounting plates fastened to the side of the cabinet (see attachment).
#4 -This system offers an array of mounting plate thicknesses to correspond to the inside face frame dimension. Each of these plates are fully cam adjustable in all directions. The hinge used can be either soft close or self close.
Regarding the under mount drawer slides, any brand will work in an inset application. Some perform better than others due to the adjustability of the slide. The Salice Futura under-mount slide features six-way independent adjustment located in the front locking clip. It is very effective.
If you think about it, zero protrusion is actually impossible with inset doors. The door will naturally protrude into the opening by at least the thickness of the door when doing inset doors.
There are a couple of good, adjustable pilasters on the market to mount your roll-out shelves. One is made by TennTex (plastic) and the other by Century Products (wood). You should be able to find both at your local distributor.