One of the long missed features of GtkUIManager (at least from a complex application perspective) is menu merging. This is something that gets heavily used in “plug-in oriented” software. And as you might expect, a large code-base will often migrate into this direction simply out of code hygiene.
I implemented something akin to this in Builder so that plugins could easily merge into the application GMenus used by the application. You can find the header and source at egg-menu-manager.h and egg-menu-manager.c respectively.
To make things easier for plug-in authors, we have a feature similar to the automatic resources in GtkApplication. Just place your menus.ui at /org/gnome/builder/plugins/:plugin-name/gtk/menus.ui and it will be automatically loaded and unloaded with your plugin.