As designed Upgrading an add-on doesn't update template modifications status

[Lior.]

When upgrading an add-on, if a template modification was enabled in the previous version and is now disabled (or vice versa), the changes aren't reflected.

Not sure whether this is by design or not, but at least in my opinion this behavior isn't really what you'd expect.

 

[Mike]

This is going to have to be as designed as it was set to allow users to control the modification status and maintain it across add-on upgrades. It accidentally expands to cover this case as it wasn't generally expected that add-on developers would change the active state on particular modifications. (You can of course bypass this by changing the modification key.)