Hello,
ok, I have tested this now with Joomla 1.0.x and yes, you are right.
In Joomla 1.0.x it works like this - the metadata on the homepage are taken from the last article shown.
However, it works in the same way with/without SEO URLs, so JoomSEF has no influence on this. You can only override the metadata generated by entering them explicitelly for the homepage and changing them everytime you update the main (first) article. Then, the meta data entered into JoomSEF will override the ones generated by default by Joomla.
Probably, this default behaviour is a bug in Joomla (as it has no logics). Fixing this -- so that the data of the first article generated are not overriden by the following articles, would require a custom Joomla core hack.
We could program the hack for you, but it would have to be a
paid support case.