Traditionally, CPU power has been regulated off 5V. (Even earlier, when CPUs were still 3.3V, they were powered directly off 3.3V. But these are days long gone.)
Intel, facing the steep power increase in Pentium 4, decided to move the CPU power regulators off the already highly loaded 5V rail onto the 12V rail to balance things better - with the decline of 12V power drawn by storage drives over the two decades we're talking PC, there has been less and less load on 12V, so this was sort of an obvious choice.
The extra connector exists because the ATX plug has very few wires for 12V, and these would be overloaded with the high current drawn by the CPU regulators.
Mainboard designers still were sort of free to choose what to do - CPU power on 5V rail and have an ATX plug only, CPU power on the common 12V supply using the extra plug just for added wires, or, the Intel way, CPU power on a completely separate 12V circuit that exclusively uses the 4-pin plug.