Thanks for the update
1) Regarding Stripe. First of all, are your Stripe order being switched to Processed status automatically or they still sit in Processed status.
In order to get rid of Order is changed messages, please apply the fix mentioned here:
http://forum.x-cart.com/showpost.php?p=376451&postcount=8
2) Regarding mail templates, why do you want to put templates anywhere else rather than into skins/mail/en folder? What is wrong/inconvenient about placing mail templates into skins/mail/en folder?