Yeah, just try the "shmup" control option if you want to see the difference, since that is, in fact, the original control setup. It's being kept in there since some people (particularly those attracted to that side of the game) are going to want it there due to the super-exact nature of how it controls. Particularly for players interested in playing on the higher difficulties.
But dont worry too much about it. Right now, any feedback that anyone can give on how the current non-shmup setup feels would be super helpful. Other than that though, just use whichever you like.