DSTT can't autoboot commercial roms since it starts up in what you could call "homebrew mode" to be completely non-technical. In other words, dldi-patched homebrew will autoboot (at least a variety of them will), but if it isn't, the homebrew probably won't load correctly (auto dldi-patching isn't going to work if you don't go through the DSTT menu or YSMenu).
An alternative option to having a commercial game autobooting would be to use ysmenu as it has a feature to autoboot an nds file, commercial or otherwise.