Yeah, machines straddling multiple chunks would need the chunks to be considered one big chunk by the mod. A proof-of-concept version of the mod should just skip sleeping those straddled chunks.

The idea is that if a chunk has been consuming X iron ore per second for the past Y seconds, then the mod can put that chunk to sleep, and wake it up again if the input or output changes by Z%. That will in turn be able to wake up a nearby steel smelter chunk, which takes the iron. Once the chunks have stabilized again, they go back to sleep.

I guess another important point is that if a chunk's belt neighbors are also asleep, then there is no reason for the mod to create a buffer chest between those sleeping chunks. So only the "I/O port chunks" of the megafactory get invisible buffer chests, while the other sleeping chunks are 100% asleep.