This is happening because the new file commands (
explorer:new-file-in-new-pane) are registered by the file explorer plugin, and the code to implement them is in that plugin. So these operations simply aren’t available without the plugin enabled. (Which is a good indication, I suppose, of how many people must be using it!)
At a glance, though, there doesn’t appear to be any reason why these commands need to be part of the file explorer plugin. The methods involved are relatively short and don’t appear to rely on any other part of the file manager. Presumably this could be fixed by moving the code out, perhaps by moving
Vault, implementing a workspace command to handle the actual operation, and then having the file explorer delegate its button and menu operations to the workspace command.