You'll need to go into "Tools | Startup..." and select your options appropriately. Uncheck "Show Database Window", and probably all the rest of the boxes as well, including the advanced one to allow special keys. Make custom toolbars and menus as appropriate, ensuring at least that you haven't left menu access to the database window.
Make a backup copy of your database at this point. This backup copy is the one to which you'll replicate your data for backup.
Now disable bypass of startup options, and make your .mde file. Make sure you don't disable startup options on your backup copy, because you want to be able to go into it and edit it later if necessary.
TMTOWDI - it's not just for Perl any more