Maybe my answer is a bit late, but it might help some else..
I agree with Paul that it depends on how you activate the look.
A composed look consists out of the composed look item (in the themes gallery) as well as the actual resources required for the look (.spfont, .spcolor, .master, etc.).
The composed look item is there so the composed look is displayed when choosing "Change the look". Once a look is applied, the colors and fonts are applied as well as the masterpage is set on the SPWeb. At least this is what happens when you do it via the SharePoint GUI.
If you want to apply the look programmatically, you need to apply the theme as well as set the master page. These are two different steps. You can do this for example by using following code (server object model) in a feature receiver:
public static void ApplyComposedLook(SPWeb web)
// note that to programmatically apply a composed look
// to a web, we need to set the master page on the web (step 1),
// as well as apply the theme to the web (step 2)
// step 1: set master page
// the master page needs to available on the SPWeb
// on which we are applying the composed look.
web.MasterUrl = "urlToMasterPage";
web.CustomMasterUrl = "urlToMasterPage";
// step 2: apply theme
// the .spcolor and .spfont files need to available
// on the site collection/root web (this might not be the web on
// which the composed look is currently being applied
SPWeb rootWeb = web.Site.RootWeb;
SPFile spColor = rootWeb.GetFile("urlToSpColorFile");
SPFile spFont = rootWeb.GetFile("urlToSpFontFile");
SPTheme theme = SPTheme.Open("My Theme Name", spColor, spFont);