The example we have as a precedent for this was when the Bloc Québécois did not have membership and was not a recognized party in the House. At the time, the proportion of questions had already been allocated among the recognized parties. But the Speaker sorted it out by using the total number in the group that was unrecognized.
So I can't speculate on what the Speaker might do in the case of a Green Party with three members, for example. But as I read this draft, it suggests that if the Green Party had three members the Speaker would be free to use a formula for what the three members would get, even if meant the same member rising.