PCI1 would be correct, this is just how computers identify the PCI / PCI-E bus to the OS. The card will also only use the amount of space in the socket that it was designed to use, depending on the type and version of the bus it's designed to for. Cards are also not always cut down to the exact millimetre, nor are the sockets themselves, these are just plastic, fibreglass, and resins.
You should be fine.
You should be fine.