Auto-updating w/out local installation

So, I've searched the forums for information about TBP's auto-update feature and if I understand this right, if you try to update TBP via the auto-update feature, all of the registry values get set to point to the portable version. However, is this really a problem if I don't have a local version installed? Shouldn't the portableapps launcher clean up the registry when it's done anyway? Maybe I just need someone to clarify exactly what that "bug" (I know it's Mozilla's code and PA can't change it and still call it TB, etc, etc, same w/firefox...) does and how it would affect me in this situation.