Following up from Mauno's post, the PDW Toggle Toolbars plugin is available (with demos) at http://sourceforge.net/tracker/?func=detail&aid=2904683&group_id=103281&atid=738747 and this functionality looks as if it pretty much does what you were looking for - I know I'm going to look carefully at it for my upgrade to 2.5 in the summer instead of the core tinyMCE init changes I had previously
And with the info Mauno has given previously about being able to set up tinymce init in the html/php of the page (therefore in the layout files of the theme), it seems like Gareth's query about controlling TinyMCE through the theme is answered too.
I would imagine also that if the tinyMCE init can be controlled via the layout file, we could also use theme settings pages to control options for that init section.
Many thanks Mauno, I think the rest of us had (small) parts of the answers but you have provided the glue to stick it all together! :D