What do you mean by "compatibility"? The various materials are no different in compatibility than normal everyday materials. Nylon is Nylon, ABS is ABS, Polypropylene is Polypropylene, etc. and they can usually be placed in contact with each other without some sort of incompatibility reaction. Some metals should not be placed in contact with other metals (electrolysis can cause corrosion), but I don't think there is any problem with Nylon in contact with anything else.
Differences in the thermal coefficient of expansion might be a problem with excessive changes in temperature.
And I think that the PA12 Nylon needs some sort of protection from UV (sun) light to prevent deterioration, but that has nothing to do with compatibility between materials.
Or are you assuming that you can print in two different materials at the same time... like forming a hinge in one material for two parts in another material at the same time in one printer? That you cannot do. You could print a hinge in one material and print the other parts in another material and then use some sort of attachment process (nuts and bolts, epoxy, etc. or maybe even a press fit of a post on one part into a hole in the other part) to attach the parts to each other after the two totally different print processes are done. You would have to order the parts and do the assembly yourself. (I don't think ShapeWays is set up to perform such post-print process.)
I don't think you can print one object attached to another object, like print a nylon part, then put that part in the ABS printing machine and print something on the nylon part. Precision placement of the 1st part in the 2nd machine is probably beyond what the present processes are capable of.