I created a new save game with a large number of planets, and selected "Any planet start" to start on Muluna. This resulted in the starting planet being Lignumis while starting tech tree being Muluna.

If you look at the tech list on the left, you can see that wood science pack is available so I think it is possible to play. There is no explicit compatibility for this combination. The requirement for wood when landing on Muluna could be problematic. Check the settings for Lignumis to disable some of the wood requirements. If you have the Lignumis Director's Cut mod enabled, you should disable it.

You don't get it; I started on Lignumis world instead of Muluna despite it being the selected starting planet.

I totally understand. It is as intended. With APS you move Lignumis away from Nauvis to another planet but you still start there. Lignumis is meant to be played as the starting planet because it's main thing is the burner stage. If you don't want that you need to add Lignumis at a later point in your game.