I kind of achieved what I want...I deleted the Default.tlo from my templates folder renamed my layout to Default. My layout now loads on startup.
Note that each time you start the TD, it checks files that are included with it against what is in your Data Store, and copies files if (a) they are missing from your Data Store, or (b) the file in your Data Store is older (this makes sure you get new files in your Data Store if you upgrade the software). Therefore, the "Default.tlo" file could be written over. Therefore, you might want to be sure you've got a backup of your modified Default.tlo file.
I think I should probably add a preference to specify the "default" layout file, much like the default tournament file.