Using covers for redstone control really seems like a better idea, but also means that there would need to be only one type of combustion engine, which is maybe a good thing to keep one block from being too complex.
Using covers would also provide an easy way to provide oxidizer to the engine using an air vent cover directly on the engine and not having to pump it in with pipes, although that should still be possible, as that would allow for use of oxidizers other than air.
When the whole spark-ignition idea falls away, starting the engine would probably be best done by providing rotational energy to it.
Anyhow, looking forward for what the future of Gregtech holds.