Very likely the onboard PATA controller is connected via ISA. I had to enable the ISA PATA support during the kernel configuration for Linux to recognise it.

In this case, there probably won't be any benefit of having additional ISA controller cards.

This is very very possible.

What I wonder is whether the onboard chipset is slower than the ISA bus - and whether using an external card would eke out a tiny bit more performance.

Apparently the ISA bus can stably run at up to 8MHz.

It's not on-point but I found this thread that discussed SCSI controllers that was kind of interesting: http://www.vogons.org/viewtopic.php?t=36001

This project is really awesome btw.