@phenomlab No worries, this is still a pain point for me.
I have been using above technique on a couple of forums via widgets but it is not ideal. It works well for desktops and larger screens but for mobile we have to push the secondary menu items into the top default menu (stock menu) via JS due to the real estate issue. So yes it is possible, but not ideal as it doesn't load sometimes for mobile users if there is a js error in any of the third party services (like ads).
I also tried updating the stock header via persona tpl files, but i've been burned as the theme structure updates frequently with new releases. I've learned to avoid overwriting the templates.
The best approach would be to have this ability in the core to handle either multi level navigation or a better responsive setup which can hold relatively larger number of menu items.
Mega menus are pretty common in majority of websites these days and if nodebb team supports them it would solve the issue. e.g https://geedmo.github.io/yamm3/