Back in the day there was no backplane and the only port on the mobo was the AT keyboard port so that was the only hole in the case. The rest were punchouts for parallel and various serial ports that would be connected to the mobo via ribbon cable. When the first ATX mobos came out they kept the punchouts for the backplane but that required all the manufacturers to use the same port layout so that lasted all of like 2 years before the pop-in shield became the norm.

How are the new ones getting around the different port layouts?