Thanks for your question! Currently, there's no admin option / setting to make a particular blog the default template site. However, if you aren't afraid of peaking in the code and making a simple edit you can hard code this to any site you want (it will still be changeable in the drop-down).
Around line 164 change the number 1 to whatever site ID you want to be the default selected:
$source_id = '1';
It should work fine with custom table prefixes as long as all tables honor the setting you've configured in wp-config.php. Some plugins don't honor those and create tables with different names. In those cases there might be issues. But, the Cloner uses the configured table prefix in it's code.
Still - let us know if you see any issues!