I didn't see anything specifically in the SDK that discussed this in terms of JS.
I assume that these buttons are created with "app.addToolButton". Buttons created with this function in a folder level script are loaded at Acrobat startup and placed in the Add-Ons toolbar/toolpanel. However, buttons created with this function outside of a privileged context are placed on a floating toolbar, effectively grouping them into a single toolset. Create a folder level script that makes a single button or menu item that when pressed, will run non-trusted code for creating the tool button set. The lifetime of the floating toolbar is tied to the current document.
This can also be done with plug-in assist for creating either a custom menu item or toolbutton category. In the case of the toolbutton category you'd also need to add buttons with the plug-in.