As has been said, runout reduces the long-grain stiffness of the wood, so, in theory, you need to leave it a bit thicker to make up for that. I have to think it might cause more porblems with cold creep as well.
To my mind, the biggest problem with runout is what happens when the bridge pulls up. As the back edge lifts the runout on one side allows it to peel loose more easily, while on the other side any top fibers that stick to the bridge dive down into the top, and sometimes take out a pretty big chunk.
In addition to that, runout makes it much harder to get good Chladni patterns, or clear tap tones, on the top, if you use that sort of thing. The stiffness characteristics of the two halves of the top are enough different that you end up having to carve the braces asymmetrically to get the top to vibrate right.
Of course, there's runout and runout. Runout happens because the tree grew with a twist, and the twist can increase or decrease, or even change direction, as the tree grows. The 'stripe' figure you see on mahogany and other tropical woods is caused by periodic changes in the direction of the twist. Spruce trees can do the same thing, although I've never seen it that pronounced or change direction more than once or twice. Those can be the best tops, though, if the runout is not too great.
Often the treee will start to grow straight, and then develop more twist as it gets bigger. In that case a 'heart match' will minimize the visual impact, and strength problems as well. You still get the light reflected in a diagonal stripe, but at least it's not two stipes that don't meet in the middle.
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