You see the problem in this case, that your damage comes from negative bullet resists that you apply on enemies. Thus, yes, making all your resist items not work, while APR procs, is the problem. But it's totally does what it says. If you want to use this item just build around weapon damage.
If you are going to buy APR, then just buy straight weapon damage. And read item's descritption: Your Bullets have a chance to become unavoidable, piercing through enemies and ignoring their Bullet Resistance.
https://forums.playdeadlock.com/threads/armor-piercing-bullets-and-other-items-compatibility.64899/#post-127011 if it's not fixed from back then, then it's intentional. It literally does what it says in item description. Hi from reddit btw.