It probably depends considerably on the design of the coilover. Yes, it's best to keep that bushing in there, as the factory geometry will put strain on the shock shaft otherwise.
Suberdave has some good info on his website here: http://wordpress.suberdave.com/?page_id=54 It looks like the Tein system has a long enough shaft to maintain the bushing. But you can see he had to adjust those coilovers way down to make up for the mounting modification.
Either one could be. Also, I have had tires partially fail due to bad alignment, where some of the tread separates from the steel belts. Makes a bubble in the tread, you can see if you jack the wheel you so you can turn the tire, and watch all the way around.