Not to be a jerk/troll, but ultimately I don't think there are good answers to the questions asked by the OP. Even on the director commentary, Bluth can't really explain why he went with a magic stone, and his lead art director rakes him over the coals regarding it. So were left with a lot of speculation--here are some of my ideas (instead of trying to make a plot work that doesn't):
1. Bluth was trying to flex his muscles after leaving disney, and there's no doubt that he poured his love into the animation in this film. The problem is, were talking about rats on a farm. That's a whole lot of drab colors. Bluth took the little bit of color mentioned in the book and turns the rosebush into another emerald city. I suspect the ending was another opportunity to introduce a lot of colorful special effects.
2. The real ending to the story would have been more of that depressing 70's angle that just wasn't what the 80's had already become. Not too long before NIMH, Lucas had proved that you can make summer blockbusters by making bright, happy, high action films. NIMH however is at times ponderous, weighty, even philosophical. Bluth carefully trimmed a lot of that out, but ultimately that meant the ending no longer worked (plus, it might have been considered too dark for kids.) Instead, we have a magical happy ending that really is magical because Bluth just made it up while tossing the ending of the story.
3. This one is a bit of a stretch; but just consider other films being made at the time. I do think people on the team undoubtedly loved the original NIMH story, but remember that the rights had sat on the shelves for some years and it may be that Bluth very much wanted to do a different kind of film. One with more action and magic. When I consider elements like the owl/nicodemus connection that Bluth says he just made up on the fly because he thought it was cool (obviously paraphrased), it shows that Bluth was considering a very different film and the working plot was just a starting point.
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