Ok, I have a 02 gtp, stock, it has a low end knock/rattle, I have knowledge of rod knocks since I've had 2 in my 97 gtp that I used to own, this sounds similar but not the same.
The 97s symptoms were lose of power, heavy knocking sound, low oil light, knock traces rpms. My 02 has no power loss whatsoever, the supercharger squeals the tires no problem, no SES or any lights, sounds at idle are lighter than a rod knock and when rpms increase it's more of a rattle (like shaking a can with a metal ball/bearing in it) it's not random knocking, it's rhythmic.
I think it may be something in the trans, or attached to the trans (flexplate, torque converter bolt maybe?) My trans has lost it OD as well but that's because it wasn't hardened when made by the manufacturer.
Btw, to give perspective, when my 97 got it's first knock the engine cracked within a month, the second knock was fixed due to warranty which happened in a swapped block 2 months later. My 02 has been knocking/rattling since June, sooo Yeh.