There is a dropdown menu in the toolbar on top, there you can select which kind of validation you prefer.
XHTML 1.01 Transitional is the default one, but you can select a different one for your frameset page, XHTML 1.0 Frameset. That way you shouldn't get any errors.
Using master pages could work, but that would require a lot of work I think. Since essentially they become the same page, just with different content. And if you're interacting with the map you might endup with way too many full-page postbacks (reloads) so I think either an iFrame for the map or frameset is ideal.