Like Jim said, kick-out flashings are still needed.

Those through penetrations don't look right either. Might not leak now, but could be problematic in the future.

Through penetrations are difficult on metal roofs. The standard is similar to what you have there, but not my favorite as it relies on a gasket. I prefer to see it done similar to shingle flashing. I know people disagree, but if done correctly, if is foolproof.

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