Not sure this helps, but my old set-up for a Pullrite Superglide hitch had four removable pins that went thru holes in the plastic bed liner, the box and locked into the frame mounts. The pins were designed to allow for thick spacers that made the hitch sit directly on the pins/spacers rather than the liner. I'm making an assumption that all hitches using a pin-type of mount have an allowance for those having bed liners.
--2005 F350 Superduty Crewcab, 6.0, 4wd, short bed, 3.73 gears
--2016 Montana 3711FL, 40'
--SOLD 2014 Wildcat 327CK, 38'