So I've decided that the best way to handle it is by putting a warning on the page that links to all the different files:
HTML files are best viewed in 800x600 or better resolution. While every effort has been made to test these files with a variety of browsers and graphics settings, extreme combinations of font and screen size may display poorly.
The following browsers were used for compatibility checking:
Internet Explorer 7 (Windows XP)1
Firefox 3.0 (Windows XP and Apple OS X 10.4)
Opera 9.51 (Windows XP and Apple OS X 10.4)
Safari 3.1.2 (Windows XP and Apple OS X 10.42)
1 Not compatible with Internet Explorer for OS X
2 Safari for OS X does not display copyright information on some illustrations when the single-file version of the game is loaded. There are no problems with the multiple file version.
I think that makes things pretty clear.