why permission denied?

If TEMPLATE.Makefile.tpl has already been extracted and is readonly, then an attempt to open a file named TEMPLATE.makefile.tpl for writing would create the "permission denied" error.
If TEMPLATE.Makefile.tpl is not readonly, then that open command will clobber the existing content, but leave the filename as (the original) "TEMPLATE.Makefile.tpl".

I haven't checked whether that behaviour is relevant to what you're seeing.

Cheers,
Rob