As you mention the string orientation might be off some with the peep at the right height. I used to just split the string strands as needed, but the last couple of years I've thought about it come to the conclusion that this may unbalance the string so now I do separate the colors. If the string is off then I put on the trusty Bowmaster press and ass or subtract a 1/2 twist or whatever is needed to get the peep orientation facing straight back. Usually I can get it right on, but if it's off a few degrees I don't mess with it.
This stuff I almost always do outside at my archery club and that's where the Bowmaster comes in handy.
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