The first spot - in the overhead cabinets - is normal. The aluminum in there has not been bonded in either my 2002 or my 2006 TM. I've thought about gluing it in place, but never got around to it.
I'm less thrilled about the join job you show in your photo. If it were mine, I would pull all the staples, flatten the wrinkles in the edge of the sheet, put on a bead of RTV/silicone caulk at the overlap, and screw/staple it back into place. What your photo shows is not in any way a problem, safety, structural, or otherwise - but it sure is sloppy workmanship. I think that with a very little effort, your dealer could be embarassed into fixing it for you.
Bill
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