An SSK will generally change the mechanical linkage of the shift knob to the rod that connects to the transmission. The throws are shorter, but in many cases they are also harder. Unless you're a wimp you'll be hard pressed to tell. Some even like it harder to shift. Vibrations and other such nuisances are probably the result of a cheap kit. Try to stick with some of the well known manufacturers. Also, things may be stiff right at first but get a bit smoother after a while, depending on manufacturer.
Yes, you can keep your original shift knob and boot. But I'd rather change it anyway.
Sometimes a heavier shift knob helps smooth out the shift throw. I've heard some people say that this could eventually hurt the transmission just like resting your hand on the shift knob while you're driving. I've never heard of any problems with a heavy knob. Maybe someone else can chime in. BTW, unless you modify the new shift knob yourself, you will lose the nice knob face lighting up at night.
I haven't heard of any warranty issues from anyone but I'm sure if BMW finds out they could try to use the SSK against you. I believe it would be legal to deny warranty coverage only for those things that the SSK could be responsible for, like a broken transmission.
In fact, BMW has their own SSK. It may be only for the other 3 series and not the M3, IDK, ask your BMW parts department. There is at least one third-party SSK that I know of that is available right now. I'm sure others are working on this too if they haven't already released it.
Cheers.