[Duugu]

The action buttons inherit from ActionBarButtonCodeTemplate and ActionButtonTemplate.

The old and the new ActionButtonTemplate sets OnClick to the function SecureActionButton_OnClick.

The old ActionBarButtonCodeTemplate doesn't had an Onclick script.
The new ActionBarButtonCodeTemplate sets OnClick to this script

<OnClick> 
    if (not self.draenorZoneDisabled) then 
        SecureActionButton_OnClick(self, button); 
    end 
</OnClick>

I've read somewhere that the 'inherits' attribute just copies the tags from the template. So, with using two templates something that is specified in both must be overwritten. As Blizzard specifies all templates from the most common to the most specific from the right to the left I guess again that the tags are copied from the right to the left.
Keeping that in mind I would say it overwrites the Onclick from ActionButtonTemplate (as the 'inherits' attribute is "ActionBarButtonCodeTemplate, ActionButtonTemplate").

That means your code

local button = SecureActionButton_OnClick
 
        local function register(val)
            if val.IsProtected and val.GetObjectType and val.GetScript and val:GetObjectType()=="CheckButton" and val:IsProtected() then
                local script = val:GetScript("OnClick")
                if script==button then
                    val:HookScript("OnEnter", function(self) bind:Update(self) end)
                elseif script==stance then
                    val:HookScript("OnEnter", function(self) bind:Update(self, "STANCE") end)
                elseif script==pet then
                    val:HookScript("OnEnter", function(self) bind:Update(self, "PET") end)
                end
            end
        end

won't trigger as the action buttons OnClick is not longer equal to SecureActionButton_OnClick.

Maybe you could fix this with

local button = ActionButton1:GetScript("OnClick")

I'm not sure if this is correct. It's just a guess.

btw: What is draenorZoneDisabled good for?
[e] Ah, it's for handling garrison action Buttons.