I too have been bitten by this “feature.” What I would like is the ability to COPY a template, rename it, then make changes that don’t affect the original template – to me, that is counter-intuitive. If I wanted those changes on the original template, I would have made them there. The whole point is to have a copy with a few changes, and not affect the original (which might be fine for some layouts).
It is very time-consuming to re-create those pages exactly, with just a few changes. It would be FAR easier to not have the pages linked to other templates.