The resistors help reduce the influence of high frequency noise (the logic input capacitance causes a natural roll off, so you just pick a value that allows you to drive at the required speed - and you're right, it would prevent any overshoot effects). The extra benefit is that although HC can handle inputs about a half-volt outside the rails, it does have protection diodes. The resistors assure there won't be much current drawn if the main supply is 5.1V or so. The reason I run much of the circuit at 4.5V is that I needed to re-regulate the 5V down to another voltage for a clean local supply, and CMOS stuff works just fine over a wide range.
I think I know how I'm going to proceed with a new Rev D prototype. Ever notice you frequently can't find that one perfect logic chip that does exactly what you want?