@David:

Hmm… not sure if I completely follow, but a couple things:

1. I don’t know nuts about .htaccess, what ships with this is a stripped-down version of what comes with HTML5 Boilerplate (as it ships, it breaks WP, so I basically started commenting lines until it worked…)
2. Most WP functions seem to return absolute URLs, not much I can do about that… at least not here, maybe in another plug-in… :-)

That help at all?

Atg