As far as your argument for the Analogue NT Mini, I don't think it has been "overlooked". I think it has been considered and rejected. At least that is my interpretation of @Jace Hall 's statements and every other thread discussing clone systems. Every thread, every request, every wall post, etc all seems to end in the same conclusion: console submissions require original console. Not my decision, but just my interpretation of every single discussion about this issue.
As as far as your argument for Gameboy, and Super Gameboy, I agree. I think games should be played on the system that they were designed to be played on. I would certainly support any effort you make in the future to get those guidelines changed.
I would also also like to see console submission guidelines tighten up when it comes to controllers. (Personally I don't see this actually happening, but I can hope.) I think 3rd party, aftermarket, later generation controllers, etc should be much more scrutinized. I also think controllers should be visible during gameplay. But I digress. My point is simply that I think there are lots of areas where console submission guidelines can and should be improved. Mistakes of the past should be cleaned up, not used as excuses for future mistakes.
Personally I like the idea of combined leaderboards. I think it is the best way to have transparency, and in the long run will probably lead to more wide acceptance of clone / 3rd party systems. Instead of keeping clone system submissions out, or keeping them to the sidelines, it brings them right in line with original hardware submissions. It allows access to leaderboards for a wider group of newcomers, etc. It removes the current barriers to entrance as the leaderboards stand now. The good thing is that it does it in a way that is transparent. I don't see a problem with that. I disagree that it is in any way similar to a subjective comparison of which basketball player is better. These are objective scores/times with concrete evidence packages. The leaderboard will show scores in their proper order, and one column will indicate which system was used.
As it stands right now, adjudicators see a clone system and it immediately shuts down. Reject or Abstain from most adjudicators. If one gets through, it will be a target for Challenge when the new system goes live. In a combined leaderboard situation, it will hopefully allow more people to actually evaluate the gameplay in submissions and not focus so much on the hardware. Hardware will be noted, and then gameplay assessed. The more gameplay that is assessed, the more it "should" lead to an acceptance of quality 3rd party clones. (And may identify poor quality 3rd party clones as well.) The point is, at least these systems will finally get to have their gameplay evaluated as opposed to just immediately rejected.