Hi Stutts - assigning the League D places first does affect the outcome and would be done exactly to avoid the type of situation you describe in your last paragraph, where the best-ranked not-already-qualified League B team would be the one chosen to fill the leftover League A spot. If you fill the League B spots first based on ranking, that team gets to play other lower-ranked not-already-qualified League B teams and it would be the fifth-best not-already-qualified team (probably ranked 8-12 in League B) that is left exposed to getting dragged up to the League A playoffs.
Now there are actually scenarios where a poor Nations League campaign could actually give a team an advantage, that could be considered unfair - say, for example that all twelve League A teams qualify the normal way, as do all four second-placed League B teams. In this case the four strongest League B teams would have to play each other in the League B play-offs, while the four weakest League B teams would be put into the League A play-offs, but this wouldn't be much of a "punishment" in this scenario as they wouldn't be facing any League A teams, just other weaker League B teams.
Of course none of this is as unfair, in a meritocratic sense, as having a Euro 2020 finals place set aside for teams ranked 40-55, as the League D play-offs does.
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