Most, if not all production houses will not allow you to tile different designs on the same board. You can tile the same design a few times, but not different ones. Now, there are exceptions of course, and perhaps your board house will allow you to do that for a cost. I don't know.
For Seeedstudio and ITeadstudio, both allow tiling of the same design, no more than 5 times (even if you can add more, they won't allow it.)
BatchPCB will allow you to tile it as many times as you want as they charge by the sq inch, not set sizes like the two above. I suppose it's possible to have completely different designs on a single board if you're going through BatchPCB. But then why bother, you can submit multiple designs and they fit things for you (again, as opposed to the previous two where you have specific board sizes to work with.)
As for logically checking pin headers, there is no way to do that that I'm aware of. However, if you're duplicating your board design, then all of them will have the same exact wiring. You shouldn't have to test the pins because EagleCAD won't magically change pin 2 for pin 6, pin 4 for pin 1 when you copy/paste a board layout
Maybe I'm just not understanding what you're trying to do.