Answers: I own a 2006 Rubicon and I have have my jeep rained on in need the top many times.Not one problem. Depending on your model year, the places are probably water proof. If the runner was not ment to obtain wet, they probably wouldn't put drain plugs surrounded by the front so you can hose out the inside and let it drain out.
you should be fine.
Wet butt cheeks comes to mind.
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