Last time I checked fee was ~10$ for each extra design, no matter if you order 10pcs or 1k.
So the reason is not about manufacturing, it's somewhere in setup process, that's why it is charged only once.
Although I can't understand the difference in setup process between 2 different designs, they just copy paste your design in a bigger panel together with other orders.
Why electrical connection matters?
The other reason that I give is because if you add many designs in cheap offers (100x100 for ex.) they loose potential money.
I have ordered a pcb from PCBWay with 6 different "designs" in it (5 mechanical for enclosure) , clearly not connected, with milling between them, mouse bites and some big cutouts for connectors, they didn't charge a penny more and I have no idea why.
Maybe because I kept pure square outline and copy pasting in big panel was easier?