It definately matters.
iPod High Rez is limited to 640 horisontal resolution, normal wide screen DVD's are often up to 1024 pixels horisontal resolution, so you are throwing away a lot of quality by using the iPod preset.
I convert all movies using the AppleTV preset, then make copies for my iPhone using the iPhone/iPod Touch preset (a bit higher resolution than iPod low res).
Sure it takes up more HD space, but USB2 harddrives are cheap these days and I want the best possible quality on my AppleTV and the smallest filesize on my iPhone.
Even HD TV-shows from Apple come in 2 versions (both are downloaded when you buy an HD show) - a "SD" version (640x480) and an "HD" (720p) version so this is the way Apple does it as well.