When I open a Word 2003 doc-format document and directly save it in docx
format, I get instant access to Themes, Word 2007 equations and so on.
Do the themes (if you use them), etc. get saved if you do that? Do colours,
say, not get converted to absolute colours when you save as the document (in
whatever format) is still in compatibility mode? I haven't dug into this
lately, so I could be wrong, but that is what I thought was the major
difference.
If I open the same document, convert it and save it, and then compare the
resulting XML-files, I can find only minor differences in the files
footnotes.xml, fonttable.xml and footer2.xml. The difference is in
rsidDefault values.
The initial differences will be minor. Where things start to differ is when
you start to use features like Theme colours or fonts.
The Convert doesn't really do much (visible) itself - it prepares the
document for having new features saved in it, when you use them.
You can ignore rsid values - they (or the equivalent) are in doc format
files as well and the actual values are irrelevant.