It was clear when the merger was proposed that this was going to be an issue. Several people pointed it out so it shouldn't be a surprise. The BBs ignored it and now we have the current situation, which will get worse because it will soon spread to the NT level.
The consolation tournaments will be particularly affected because they are already so dependent on the draw. The only practical solution now is either to remove countries that can't field teams at either level or as others have said, seemingly since Utopia was created, take players from there. Personally I expect the problem to just be ignored in the future as it has been so far.