Hi,
About modifying original templates, I agree and desagree
I agree when you want to test quickly a small modification that you hope will not be too hard to do.
But I disagree for the long play and for the big play : first it will be hard to maintain : every time you update your SME, you'll have to apply your modifs again after update. So, to keep even a mittle modif, you'll have to go the "template-custom way"
Second, if your modif is a tricky one, it's hard to keep things clean : you'll have to keep a way back to the good template in case things go wrong with your code ; so you must have a copy in another directory (due to the way templates work, you cannot just keep a foo.sav in the same directory)
And guess what ? It's just why you have a template-custon directory : this way, the template directory keeps clean.
IMHO, if you want to make your modifications avalaible for the long time, at the end, you'll have to "template-customize" , so do it at first. It isn't difficult to do a mkdir -p and a cp of the template you want to alter ?