Those short shifters have a needle roller instead of a nylon bush. It's nore precise and direct but there's always going to be more noise and vibes heading up the gearstick. Nothing to do other than change the stick for one with nylon bushes if it shits you that much.
It's possible there's some abnormal noise in the box that's travelling up through the stick as well. The nylon pads on the shift forks inside the gearbox wear out if you drive with your hand leaning on the stick too. Transfer bearings can fail too and that can make a noise in the cabin amplified through the shift lever.