I don't think it is a question about who can change the pin outs of a connector when they see fit. The question is if it is a good practice to do so. As a PCB designer it is the designers responsibility to design a board that exactly represents what is to be built and assembled. If I send a design out that has the silkscreen mirrored and they put the connector in wrong who's fault is it? They built the design as I told them too, or as the data states. What is correct the pin out or the silkscreen?
I know the assembly house should call when a red flag is tripped but how many do, and who is to say they are going to get the same engineer or designer who knows what is going on with this design?
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