this bears more investigation, but metal is good at transmitting vibrations, so its possible its just transmitting noise from the transmission. its also possible its just vibrating on its own.

in about 99 we had a couple of miatae come into the dealership with exhaust noise, and we replaced exhaust parts, until we got a bulletin to replace the hub sliders in the transmission. it turned out that Mazda used a larger clearance between the slider and the hub, to make it shift easier, but the side effect was that they would vibrate and make a noise that sounded like a broken weld/baffle in the muffler.

so the aftermarket shifter noise could be a few things, and it there is something the stock shifter does that avoids the problem, mostly. my first Rx7, an 86, had a shifter rattle, completely stock.