It was probably more like having some engineers and guys in shop/factory work weekend to meet the demand, on top of what they were already supposed to do.
In order to create a prototype with a port in a different location, they would need, at the very least, to produce a one-off motherboard PCB, and a one-off injection molded case. That they could justify doing so to produce near production quality results for a small order either indicates impressive manufacturing flexibility, or an inefficient manufacturing process.
Your assumptions that they would need to redesign and tool up for brand new complex motherboard and housing parts are incorrect. This is a foolish way to accommodate a request to physically move a connector.
Their process is implemented for flexibility first, then for mass production. Look at Toyota fabric [1]. Do you see lot of advanced robots to reprogram for each new model?
So how is/was Fujitsu's laptop manufacturing tailored toward flexibility? I want the details. If all you can do is passive aggressively repeat vague ideas that were printed in mainstream management and manufacturing texts decades ago, don't respond at all. Nobody cares about or wants your input.
And you think that someone from Fujitsu (where it's 8 in the evening, BTW) is going to jump in here and explain their factory layout to you, because you've put your foot down? The best general answer you are going to get is "They made it using whatever process they used to make prototypes. Probably". You want names, ranks, and serial numbers - try writing to Fujitsu. Preferably while being more polite.
Or... that it was an option for port placement they'd already considered, and they pulled an existing prototype out of the library, which seems more likely to me.