The vacuum table is indeed considered a consumable since it gets damaged by drills and contour routers, at least that is assuming your S103 works the same way as my S63. It's an extremely poor design, and the vacuum table is ultimately unnecessary since you can also simply tape your board down to a carton board substrate (as was the case for Protomat 95S/II or C100). The depth delimiter is controlled by a stepper motor, and you can simply configure the thickness of the carton board or MDF you're using in software.
Prototyping multilayer PCBs is hard because you'll need thinner FR4 copper clad board, prepreg laminate and a device to press them together under elevated temperature. You'll also need plating tanks for via's to connect the inner layers. In my experience, prototyping multi layer PCBs in house isn't worth the equipment and consumable you'll need for it. You can buy hundreds of 4 layer PCBs in China (wwww.pcbshopper.com is good start) for the cost of all the equipment you'll need to make your own multilayer boards.
Prototyping double sided boards is fairly easy, it's done in 2 runs: first drill alignment holes to be used as fiducials, then mill/etch top layer, flip the board and align using fiducials, and then mill/etch the bottom layer. This paper gives a good overview of the processes involved:
https://www.academia.edu/7108733/Ex...cale_PCB_Manufacturing_Techniques_for_Fablabs
That said, the newer LPKF machines (including S63 and properly also S103) are absolutely overpriced crap. Buying a Protomat S63 was my worst investment ever. Machine broke down 2 time in the first half year due to hardware failures. The solder paste dispensing mechanism never worked properly. LPKF no longer offers support and forwards customers to its incompetent subcontractors. And then there is the CircuitPro software, which is littered with bugs and crashes as soon as you're trying to do something out of the ordinary.
I can highly recommend a Protomat 95S/II, mine is a second hand machine from 2001 and it still works like a charm. Automatic tool changer with 30 positions, very reliable, CircuitCAM is bug free and in BoardMaster I've only been able to identify a single bug in all these years.
I wouldn't recommend to buy new LPKF machines, they're a waste of money. And LPKF knows it, they refused to take my S63 back even after I was able to prove the hardware- and software failures. Worst customer service ever.