It does matter. If a website knows that you use SuperGenPass, they can conceivably guess your master password if it's weak as a direct result of SuperGenPass using a fast hash function to generate the site-specific password.
In a scheme like this, the "real password" is the output of a hash function (albeit munged a little bit), so choice of hash function is important. I'm not a cryptographer, but really a key-derivation function seems like it would be a lot more appropriate here than a simple hash like MD5.