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3rd Gen Ram Tech2002-2008 Rams: This section is for TECHNICAL discussions only, that involve the 2002 through 2008 Rams Rams. For any non-tech discussions, please direct your attention to the "General discussion/NON-tech" sub sections.
I have the same truck with a bedliner. My top was made by Astro. My bedliner does not cover the top rails, but I would suspect that it really wouldn't matter much. There is a 1/2" soft gasket that seals the top to the rail and would probably conform to the extra space a bedliner takes up. Bottom line, I think you can't lose either way. Good luck.