Let's say in an a4000 I am using a 3640 running at 30mhz vs the stock 25. With the jumper in EXT what is it actually doing?
With the jumper set to INT the motherboard generates a clock for the CPU, with it set to EXT the motherboard doesn't generate a clock.
In either case the motherboard generates it's own clock.
When you use an external CPU clock then the motherboard has to synchronise the two clocks when the CPU accesses the motherboard.