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When we remember that there is a reason that we use glue to assemble leather holsters, and it's not to keep everything in position and it's not to make it last longer (neither is correct), one recalls from our early playing with leather, that it prevents squeaks! In even the finest holsters; try building one of your best without any glue at all and re-discover squeaking.
Leather saddles squeak where the loose parts rub together; and that's what happens with a hybrid: the rubbing of the loosely connected pieces, such as loosely-set rivets or with chicago screws used for assembly.
Simple: glue your kydex shell to your leather backing, then reattach it with whatever fasteners were supplied. Why wouldn't the maker know this? Because they didn't come up through the ranks of the leather holster makers, and really don't know much about holsters at all.
You've mentioned that you've had this problem with your web belt, so it's not the belt rubbing against the holster (only a leather belt would cause squeaks against the leather of the holster).
For glue you can use the Barge you'll buy in a tube at your local hardware; or if you're a synthetics man, you will do even better with the adhesive/sealant used to hold the windshield into your car. The latter comes in black and can be applied more thickly than the leather-only glue that is Barge.