Its fine to nail through the flashing and caulk to prevent seepage. I try to sneak a 6" strip of tar paper behind the first lap of siding above the deck and let that come over the top of the flashing then nail the starter strip through both the felt and flashing. It just eliminates the possibility of water splashing up behind the siding, but if you have good overhangs it should be fine either way. The ends of siding usually tuck into j-channel or specially made inside or outside corners. I don't understand your question.
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