I’m pretty sure it is a bug.
I’ve not had reason to build a multipanel plugin with flyout menus, but I’ve tried just now with a simple test plugin, and I am seeing the behaviour that you describe.
Needless to say, my test plugin works as expected in Photoshop – each panel has its own flyout menu containing the menu items defined for it in the entrypoints.setup function.
Unfortunately it looks to be (another) bug specific to how flyout menus have been implemented in InDesign.
Philip