The new version of the HGSS pokesav (.03a I believe) supposedly has the correct output. I have confirmed that it uses the correct US Game ID, yet, for me at least, the codes still don't work anyway. Note that this does not apply to the compact version, which, as far as I know, still uses the JP Game ID.
Naturally I would also welcome any more elaboration, as I too would love to start using pokesav for HGSS.