Those are to give proportions, not exact numbers. The problem with dealing with the numbers instead of the modifiers is that the numbers move opposite to how you want them to, while the modifiers move in the same direction (as per RichW's example). By 'move in the opposite direction', I mean that if you increase the number of homers while leaving the other numbers alone, it will result in a decrease in homers in your league. This is difficult for most posters (including me) to deal with, so messing with the modifiers is just much easier.
I could be wrong about this, but I don't think changing either of those in the middle of a season will have an effect. There is some date (maybe the beginning of the preseason?) after which any changes will be applied to NEXT season, rather than this one. At least, that's what I remember. Somebody else will know for certain. That's why in my second post I mentioned posters who replay the first season over and over until they 'get it right'. And the second season should take care of itself without needing adjustment, assuming you want a modern MLB environment (which is what it sounds like from your posts).
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