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If you had it done by a professional, they could tape the seem after hemming. It's likely that you or a friend attempting would mean that everything would get hemmed in one piece including any lining, membrane, or insulation. So you're basically putting hundreds of tiny holes into the sides or bottom of the fabric.
You can spray treat them after, but that seam (if it's the inseam) is a crucial seam and on most pants is taped. If it's just the length, it's less so, but you may run into issues with the length of the gaiter and what not.
http://www.rockywoods.com/Hardware-Zippers/Seam-Sealers-Seam-Tapes/Using-Seam-Tape
I guess in technicality taping the outside of the seam would work if you retreat the dwr again after ironing. But it may look strange.