I completely agree with you. But 1 per nation would still be better than 2 per nation irrespective of the Nation's size, like the OP is proposing, wouldn't you agree?
If anything make the B3 slots based on overall nation rankings and create a second tier of international competition which is open to the runner ups or winners in their country competition, depending on who's going to the B3. This second tier competition will help determine the world rankings for nations and determine who gets 3 slots in the B3, who gets 2 and so on in the following season.
If they fix Enth, I'd fully expect the bigger nations to do well in both B3 and second tier competition and get the most slots. This system would be more similar to the current champions league...