Hi Joe. If the parts you work with are of nominal size that will fit the MT collet almost perfectly then the MT collets will potentially be more accurate than the ER collets. The reason is that there is only one interface, that of the collet in the spindle. With ER collets you must have a chuck and the chuck to spindle mount interface and the ER collet fit itself will introduce some runout, small though that may be. Bottom line is that the MT collets will give you the least potential runout of just about any other type of collet (unless you have a native 5C spindle, in which case you would use 5C).
On the other hand, if the ER chuck is mounted very accurately and you use good ER collets you can get runout down to about 0.0002" or so. The key advantage to the ER collets is that you can grab onto parts that are non-nominal size, which is usually what us hobby guys work with, so ER collets are very popular.
Neither the MT collet or ER collets will tend to mar the work piece, although if you cinch down hard enough you can cause some distortion of threaded areas.
Personally, I use ER collets. I have a 5C adapter with Royal 5C collets and its pretty accurate but useful only when I work on nominal sized parts, which isn't that often and especially once it is turned and needs to be chucked up again. The flexibility of the ER system is worth what little runout I have to deal with.