... like in the PC AT, PC XT[1] or the Compaq DeskPro 386[2] that the article discusses didn't have those ports at all.
Those were instead on ISA expansion cards, just like the floppy controller that would often share a card with the UART controller for the serial interface.
[1] https://theretroweb.com/motherboards/s/ibm-xt-type-5160-64-2...,
[2] https://theretroweb.com/motherboards/s/compaq-deskpro-386-20...
Before that, when you installed a hard disk you had to go into the BIOS to specify the geometry of the drive. 46 types were already defined, to match individual drives on the market. "Type 47" allowed -- required -- manually specifying the drive geometry in terms of cylinders, heads and sectors. So for a short while some traditional MFM or RLL drives would be informally classed as Type 47 because their geometry and capacity differed from earlier drives.
My 486 and earlier systems have all I/O provided by ISA cards, other than the 5-pin DIN keyboard port which was standard since the original PC.
Details here: https://theretroweb.com/motherboards/s/dell-system-486p
But, yes, most bog standard machines would've had a separate "SuperIO" card containing serial, parallel, and IDE interfaces until the mid 90s.