You can adjust the amount of penetration into the face side of the sheet using the adjustable collar on the drill bit with these jigs. You are always going to be limited in depth of screw penetration by the thickness of the material. Perhaps you are thinking that you can butt joint two pieces of plywood and screw from the face side into the "end grain edge" (its not really end grain, I know) which would allow you to penetrate as deep as you want. The problem with that strategy is that the edge of a plywood panel isn't a reliable place to drive screws into since the plys of the panel can separate. As it turns out this isn't very strong, although its stronger if you use top quality birch plywood. The pocket hole approach bypasses this issue by anchoring the tip of the screw across the plys so even though the penetration is less the strength is greater. Bottom line, it shouldn't be a problem for good quality 12 mm material for something like a bartop cabinet, I suspect.
Now if you chose to use MDF, you could use the strategy of driving screws through the face and into the edge of a butt joint. Not super strong actually with 12mm MDF. However, you will have exposed fastener heads unless you recess them and plug them or countersink them and fill over them. More work. The pocket hole approach gives you hidden fasteners and similar strength.
If you are really looking for a bulletproof cabinet construction, you can add dowels, dominos or even biscuits which align the panels and increase the glue surface. For 12mm material, small biscuits are probably the best option but this requires using either a biscuit jointer (you have to have one) or a router with a biscuit cutting bit (painful - just say no).