Scale of mismatch is the issue - if Scotland and Japan are racking up 100ish point victories over some of these teams, what is it going to look like when they come up against the top seeds in their pools on being promoted? I'm not sure World Rugby will be too keen to see that in premier age grade competition, as opposed to the trophy were it's a little bit out of sight, out of mind.
Not sure how consistently you can rely on Tonga and Samoa getting access to higher quality talent either, might depend on whether it's a selection policy they can change or a lack of interest from those players who'd see NPC as a better setup for their development. Scale of the challenge may change their perspective a bit, but they might be more concerned with how professional the program is at this stage.
I do still think it's an important shift though getting more teams more competition at a higher level, particularly with the World Cup set to expand. It's just that the current promotion/relegation system looks like it will create unacceptable mismatches. Working out a better system there is probably the real logistical challenge, not so much the 16 tournament itself which looks very doable.