So we got back from Hong Kong today.
And there weren't any problems with my wife and son travelling there and back, using the Entry & Exit Permit type "L" (for tour groups), as individual travellers.
She didn't need to buy any endorsement from Taobao or register with any tour group, we just went with the permits that they had.
I'm not sure if a factor in being able to do that was that she was travelling and doing all check-ins with a toddler and foreign husband, via courtesy channels when available. Could have been different without one or the other.