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Hmmm, curious to know how that would be necessary...trimming that is. My rails are set equally with a small gap at the tailgate. They're not indexed off the bulkhead.
In order for the cover to be in the correct position front to rear, the rails need to be all the way forward per the instructions. See #2 and #3. If you have a drop-in bedliner or anything rather thick, it might be a problem. See the note at the bottom of instruction #3.