I would say no if you have an ATX motherboard, a Molex connection has 12V, 5V and ground leads while an ATX power switch shorts two pins on the motherboard that connect to the ATX power at pin 16 and a ground -- although I am not entirely clear on your issue.
What motherboard do you have? Is it ATX or a really old AT?
When doing a bench build, I start up the system by briefly touching the two motherboard power on pins with a screwdriver -- they only use a momentary short, the old style AT cases of long long ago that used a different style motherboard required a circuit to be closed -- like a light switch -- the entire time that the computer was on.