You can control how layouts are handled on the Preferences tab, in the "Loading / Saving" category.
You could, for example, configure the TD to automatically load a layout saved with your tournament without prompting you each time. Or, if you have a "default" layout you always want to use regardless, you could configure it as the actual "Default Layout" (press the Config Files button on the Preferences tab), and configure the preference such that a layout is never loaded with a tournament. You could then turn off the feature that saves layouts with tournaments, which will make your tournament files smaller and faster loading.