When applying the tick in the checkbox for "Prevent template modifications from being automatically applied", I'm finding after saving and then returning to the template, the tick is missing.
(I'm assuming that by applying that tick it will stop any template modification relating to that template from working in a particular style).
Fixed now. The issue was that if you check that box and attempt to save without actually customizing the template contents, it would ignore all the changes (transparently) and not save anything - which is by design, but I can see why it could be confusing.
So, now if you enable the checkbox, it will save a custom version of the template even if the contents are not modified. Just so you know