To answer your question in another way, it would not surprise me if passports valid less than 6 months won't work in e-Channel. What I would NOT expect is a situation where e-Channel would let you through in the same situation where you'd be blocked if you dealt with an immigration officer.
Then there's another point:
But to catch my flight in Hong Kong, I would need to enter Hong Kong
That's not true. You can take a ferry from Shenzhen to HKG airport. You can do so ONLY if you are departing from HKG on a flight, and also you never enter Hong Kong by doing so. Your outbound flight from HKG will be checked at the ferry terminal in Shenzhen, where you will exit China. Upon arrival at HKG, they will re-check your onward flight, and assuming all is well, admit you to the airside departure section of the airport, without ever having entered or departed Hong Kong as far as Immigration is concerned.