Dan,
"Guidelines" are not "instructions" ... legally (speaking as an MBA and NH certified paralegal for over 20 years). Warranty intact, but read what is guaranteed. I chose the highest level coating/paint offered by the manufacturer.
Not sure what you mean by "put under the raised section of metal roof to take up the space". The panels are flat unto the shingled roof. The screw's tension is determined by the gasket "squashing/not squashing". I used a standard screw from the panel manufacturer; 14-10X2 ST 17 ASTER W/W OXY PNT; a #10 WOODTITE fastener with gasket. There was no problem getting grip. The issue is/was, not to over-tighten the screw, and compromise the seal.
Another issue was/is if the panels are placed on purlins or strapping, say 2x4's, and the "recommended" spacing is wrong, what stops the panels from bending when they are walked-on? I spaced at 12" on center on the ribs, and doubled at the termination points (end of panel). I've been on the roof several times to upgrade chimney attachments, get rid of Satellite antennae, etc. and have no problem, nor qualm about panels bending or having a reverse bump.
Caveat; when roof is wet, very slippery.
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