Default First Layer as Layer 0

Scripting might not be necessary. See if it works to build this Action (I haven't tested it fully):

1. In the Actions panel, create a new action. 

2. Insert the command Layer > New > Layer from Background. That is the command that converts a flat Background to a layer with transparency (Layer 0). Remember that the Actions panel menu (the menu that pops out from the top right corner of the Actions panel) has a command called Insert Menu Item, so you don’t actually have to record this part, just insert the command. 

3. Create a separate new action.

4. Open the Actions panel menu and choose Insert Conditional. 

5. Set it up like the picture below, where if a document has layers, nothing happens, but if it doesn‘t have layers (it only has a Background), it runs the action you created in step 2.

If you wanted this to run every time Photoshop opens a document (like when the plug-in sends a file to Photoshop), choose File > Scripts > Script Events Manager to open the dialog box that c.pfaffenbichler mentioned, and set that up so that on Open Document, Photoshop runs the action you created in step 5, which checks for layers and if there are none it converts it to Layer 0.

If you need it to be smarter than this, like only converting background to layer for the specific files received from the plug-in and not every file that comes through, then it might need more conditions that Insert Condition doesn’t support. In that case you will have to write a script and add that script to Script Events Manager instead of this action.

You could create a Script that changes the Background Layer of a flat image to the Open event with Script Events Manager. 

What should the Script do if an image has more than one Layer etc.?