I'll submit a quick PR as a PoC.  Tal emailed with additional ideas about menudefs, so I agree that another issue would probably be suitable for more discussion.

I haven't looked at the extensions too closely yet, but the insert you're referring to is actually on the 'values' part, so it's not an issue.

mainmenu.menudefs[0][1] refers to menu item 0 (file menu) and the [1] means the nested list of tuples within menu 0.  I learned that while converting to a dict.

A trickier one is this because it changes the menus:
        mainmenu.menudefs.insert(0,
            ('application', [
                ('About IDLE', '<<about-idle>>'),
                    None,
                ]))

But I think this will work for that:
        appmenu = {'application': [
                        ('About IDLE', '<<about-idle>>'),
                         None,
                        ]}
        mainmenu.menudefs = {**appmenu, **mainmenu.menudefs}