Good question!
This rule of mono patterned panels is unfortunately quit common. The newcomer company is not pulling any crap. for they are just going with the flow. There are manufacturers in the field who will oblige your request, but then you will need to way the options about surface area, vias, layers, mask or not to mask, silkscreening, price, and time all over again. Sorry, I can not provide you with an all around source at the moment.
Possibilities are
*Design Rule Checking
*Netlist Test
*Batch processing with othe orders
I am more sorry that the little people have to juggle while going through hoops and ladders for a couple of protos. Even some "No Touch" services, no design rules or checks, are not allowed muliple patterns.