The very low prices are only for bare PCB's. (2 copper layers, 2 solder masks 2 silk screens, no solder stencil)
What is your BOM cost for the parts? uC, LCD, lcd driver, etc. Have you considered that in your price?
The problem with small quantity PCB's is that assembly takes a relatively big amount of human intervention. There are problems with standardization to communicate footprint orientation from EDA software to assembler. For making of the PCB it does not matter, the pattern of the copper to be etched and other layers are defined well enough, but once you start assembling, your QFP can be rotated and your diodes can be backwards. Even if it takes only 5 minutes to check this, all profit for the assembler would already have evaporated. Add to that the labor to put the bare PCB's on the assembly line and packaging the PCB and send them to you and it's amazing it can be done for such a low cost at all.
For assembling these low prices are also only possible for parts that are already on the machine. Ordering custom parts for you, taking off the packaging and adjusting the P&P machine so it can pick up your custom parts can not be done for EUR6.