Stiffer bushings will talk more than softer bushings, If it bothers you you can get some sound Isolation goop like dyna-mat and apply it to the under-side of your center console and alongside of the trim up to the shift boot, all that plastic acts like a horn and amplifieds the noise coming from your transmission tunnel. If you want it quieter than that you can install a second shift boot under your OEM boot and add some recycled denim insulation between the two.
Most aftermarket shift kits will increase noise from the transmission to the cabin. I have tried a few things over the years but eventually like performance exhaust you just get used the sound that a performance car makes.
13 WRX Hatch - Torqued Performance Stage 2+
Slow is Smooth > Smooth is Fast