As IndigoTea said you can assign a different skin to your home page so you could have the Flash only in the master page of the skin used on the home page. If you are concerned about maintaining 2 sets of CSS that is almost the same, you could actually put the CSS in a common location and use it in both skins, see the article Understanding the style.config file which explains how to do that. Each skin folder would still need its own layout.master, theme.skin, favicon etc, but the CSS can come from a common location.
The main benefit of keeping the CSS in the skin folder is for easy redistribution of the skin it is better if it has everything it needs in the same folder so you can just copy the folder to copy the whole skin. But I think for most people designing their own sites redistribution of skins is not a primary concern.