I just recently installed a new one. Mine fit flush as well. The Master Parts manual describes those as having multiple lengths. As one of the previous posters stated, it may work, but it sounds like if it bottomed out before being flush, it isn't the correct length.
If it is just the length and other than that it is ok, you could take a Dremel (enabling you to get inside the flange and bushing) and cut it off closer to flush. This would ensure it doesn't bind the u-joint.
