Is it good design to limit an application like this, which will control another application, to a rather enforced methodology?

I don't know. The reason I don't know is that I don't know what the ultimate design goal of the project is - and who should be using the templates (and for what goal). What is going to be more important, doing the simple things, or the hard things? Sometimes it's worthwhile that hard things are more difficult to do, in order to keep simple things simple. Sometimes it's ok to make simple things a little harder so that hard things aren't too difficult.

Who's going to the user of your template system, and what is (s)he supposed to be doing with it? That should be the most important question when designing your system.