I've replicated this locally with 2 quarries, each powered by an engine with a single bucket of gaseous fuel in them. One of them is constantly powered, and the other uses this redstone repeater type setup.

While the redstone repeater setup doesn't generate any additional heat it also doesn't generate power for the ticks when it is turned off. In addition the engine looses stored power while it is turned off which means that this doesn't actually help very much.

Thanks. I just wanted to make sure this was something to be concerned about or not.