Generally yes edits should be spaced out to avoid overwhelming the front page, and typically questions asking about the differences between two editions have been tagged edition-comparison plus the two editions concerned.
This question seems to be jumping the gun however. The first question we ask about this shouldn't be “How do I handle this restructure?” but instead “Should we restructure Mutants & Masterminds's tags, and should we do it like this?” and as far as I can tell that step got skipped completely.
Our Dungeons & Dragons tags have some special handling to use the dungeons-and-dragons tag only to discuss the system broadly and not for questions about specific editions, but that's not the default way to handle things, only the most visible. It's the rule we chose to apply to D&D's tags to help us keep things manageable in its expansive landscape, and other systems might have similar tagging rules applied if they need them.
The default way we handle system tags is the default for all tags, “do whatever seems right”, which has shown up in a few past discussions about different systems:
That same idea came up in a question about how to structure Mutants & Masterminds in 2014:
Back in 2014, we had an actual discussion about how we wanted to handle World of Darkness system tags as we looked to reorganise things, which is essentially what I'm suggesting should be happening here first:
The mutants-and-masterminds tag contains instructions to handle it like D&D, but as you note, you added those instructions just before asking this meta; they weren't pre-existing. We should be cautious about essentially unilaterally restructuring a tag when that might not even be necessary or wanted by its other players. Granted, you're one of those players, and that counts for a lot, but nobody else has apparently had a chance to weigh in on this yet.
So instead of going straight to “I'm restructuring this, how should I do it”, I suggest the first conversation should be whether it's even helpful to do this so that Mutants & Masterminds players have a chance to comment on how their game should be organised on this site. This will also let people weigh in on your question #2 about what to do regarding a first edition tag.