My Polaris doesn't mind the cover. There's definitely some squeaking as the hose slides around under the cover, but I haven't noticed any actual problems. I think the cover is 8mil but at this point I'm not sure.
If you have the cover in sections, I would run the sections so the long side is against the wall that has the Polaris fitting in it. That way the gaps between sections are less likely to get dragged by the hose as it moves around.
--paulr
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