I first thought that this is clearly a useful change, that essentially all applications of format=template would want. Now I found that I actually have various cases where format=template is used without link=none, simply to display links in a different layout without doing any smart processing in the template.

So changing the behaviour will break such uses of format=template, and it will potentially cause confusion again. So some uses of the format will be more complicated and confusing either way. Could there be other ways (e.g. better documentation) to address these difficulties?

Your P.S. was already fixed (there was a separate bug there).

I agree that link=none should be separate from format=template; as long as you are aware of them, it's no harder to match the automatically made links than to match the plain format -- and if you only want to modify some of the values, it's nice not to have to manually link-ify the other ones.

A possible improvement to help debug problems would be to have a note come up on preview if format=template is used without link=none, reminding the user that automatic linking is enabled.