The issue is under heavy load (i.e. full throttle / grabbing gears), there is a bunch of flex in the factory trans and engine mounts. This is great for vibration damping, but it's not great for power transfer / consistency. The biggest problem is under load going to 3rd & 5th gear.....you have to feel for it a bit, it's not a quick engagement.
The trans bushing is suppossed to help with this, but by stiffening up the mount points you end up with some negative effects (noise, vibration, harshness). When I looked at the OEM mount, all the voids in the rubber are soft spots, no hard contact....except the bottom of the mount in the center (the area where I removed material). This is the only spot where it makes hard contact with the OEM mount and is likely the spot transmitting the noise / vibration.
The problem is, if you want a rigid mount, you have to fill the voids. If you fill the voids with a denser / less flexible material, you transfer energy in the form of heat, noise, vibration, etc.
You end up with a trade off.... A solid mount that shifts well, but has some undesireable characteristics. Or, you leave the OEM mount alone and have a bit of notchy shifting to 3rd and 5th.