You mean putting chemical-resist black tar on the soldering side of the PCB after the board is tested? That might work. But if the board is faulty and was sent back for repair, only the producer would be able to repair it as only he got the schematics and program. The customers who bought the product wouldn't be happy. I have seen this type of protection method and the board looks really messy.
Using other Made-In-China mcu means the traces has to be modified as well as the program too. In that way the production cost would be very high. According to my friend, the maufacturer would charge very highly for any mods or cracking the codes in the mcu. But making exact copies is a different story as long as the volume and price met their targets. I can imagine how they clone the PCB. Just remove all the chips and solder masks. Take photograghs of both sides of the PCB. Use photo-shop to clean up the picture and make them really sharp. After alignment of the top and bottom sides and the vias. They can start making PCB out of it. Of course I am talking about double-sided PCB only. They dont even need to understand how the circuit work.
HP used to protect their designs using in-house ic numbers like 1820-2435. But looked like not very effective. Their in-house vs real chip numbers tables are all over the net. And besides, you need to have enough quantity only then the chip manufacturer would print the in-house numbers for you.
Allen