[development] alter theme registry, but only for some themes. possible?

[David Cohen]

I have some modules that alter the theme registry.  In practice, I could
limit these alterations to only some themes.  On a site with multiple
themes, my modules might need to alter only one or two.  However, I
can't figure a way in code to determine which themes might need these
alterations.

Ideally, I could allow the administrator to select one or more themes
which will be used.  Either by selecting the themes in a form, or
possibly by adding something to the theme's .info file.

Is such a thing possible.  In particular, how can I ensure that the
theme registry will be rebuilt after the administrator submits my form
or edits the .info file?  Is there a best practice along these lines?

-Dave

P.S. too bad drupal doesn't support post-process functions in theme...