Do you have a bunch of MeshInstance3Ds you'd like to come together and become one?
Do you want them to keep the material applied to them?
Do you want a tool that does that and absolutely nothing else?
I made a plugin for you :)
This is two MeshInstance3Ds containing one ArrayMesh each imported from Blender

The toolbar that controls this Plugin fits in with the rest of the editor interface seemlessly. Go ahead and try to make it look weird, I dare you.

As you select Nodes in your current scene, the marked box below lists any that are eligible for unionization.

Once you've selected the MeshInstance3Ds you want to join, set a name for the mesh that will be created. Identical names will have an integer tacked on the end just like any other duplicated Node name. Click the "Join!" button to commit.

Assuming you have "Show Preview" checked: you should get a preview window. Click "Continue" or hit the Enter key when it pops up if you like it. Hit "Cancel" or the Esc key if you don't.

If yes: Boom, a singular MeshInstance3D containing an ArrayMesh that's consolidated all the surface data into itself.

It's integrated into Godot's undo/redo manager. Just Ctrl-Z if you don't like the result, and Ctrl-Shift-Z if you change your mind.
Available at:
https://github.com/the-packrat/godot-mesh-union
(github is new territory to me. let me know if something's up.)