You could probably help the matter, at least in regard to New France, by having the government enforce legislations that companies were supposed to transport the actual number of colonists promised in exchange for the monopoly that had been granted to them
Well...Royal government didn't managed very well to enforce the legislations they intended for their colonies in first place, when they actually bothered with. Too far, not enough forces, not real incitative for doing so as well (it's not like the whole region was that vital for them).
A less autonom Sovereign Council could be helpful, but I doubt it could really increase the numbers of colonists : being send to Canada was actually used as a threat in the anti-protestant persecution, and it worked.
The early beggining of the stagnation of population not being present up to the XVIII, even a PoD there couldn't do something about a pressure of population, unless coupled with a PoD where Britain can't invade Canada (knowing it did already once OTL before SYW, it's going to be hard)