Everything depends on the manufacturer you're working with. Keep in mind that, whenever you're going towards custom designs, you'll immediately facing an initial set up cost ranging from several thousands to tens of thousands of dollars. So don't think of it as sending in Gerbers and NC Drill files to a PCB fab to get your boards manufactured, for this kind of work you'll typically meet up with the engineering team of the manufacturer and discuss your project requirements face to face with them.
What they typically require is a box model of the assembly, such as STEP or STL, which constrains the size of the assembly. There are no limits to the form factor and length of an FPC connector, but the larger the flex part is the more expensive the manufacturing process will be. Therefor it's usually better to optimize the PCB to keep the flex FPC connection as short as possible (added advantage: mechanical robustness) and supply the manufacturer with a complete 3D model of your product so they can design and fit the assembly as good as possible. Of course, you'll always have to provide a complete set of mechanical drawings (autocad and DXF are de facto industry standard) as reference.
Once again, however, keep in mind that you'll be facing a considerable NRE cost when choosing custom display technology, so it might be a good idea to spend some more time on re-engineering your product so that a standard assembly can be used.