Depending on the strength of the pullup required for stable operation, it could be used as an input directly. The internal pulldown on the chip should be maybe at least twice as strong for that to work reliably. If used as an output, there would not be a problem in its use.
As for pre flashing the chips, it will raise the price quite a bit, especially if they don't have the tools already in place for this specific chip. As for getting the chips pre flashed at the chip factory, I don't think that we are a large enough player for them.
If we want the boards flashed, a board edge connector could be used (think pci express) to which the board would be crammed into, and then a SWD debugger could load the first firmware at the factory in a very automated manner.