I just found that Lignumis has some code to add basic circuit boards to lv 2 drills, labs, assmblers, and inserters only when AAI Industry is enabled, and I kind of wonder why is this implemented. I mean, Lignumis already has AAI as an optional dependency, making wood recipes for lv 1 machines guarenteed to overwrite AAI recipes, so the lv 2 machines should already contain that much of wood, and it seems not so necessary to add more.

The compatibility code for AAI is rather old. And I never really played the combination beyond some testing. It is possible that it's not perfect. It made sense back then. Feel free to propose specific changes or make a PR yourself if you are able to.

I've just made an AAI re-balancing, and I found out that if the burner upgrade chain is severed, currently the electric drill etc. will have non-wood recipe plus some basic boards, which is acceptable for now as planets with urgent needs to produce these locally do have access to wood (Vulcanus, Cerys, etc.) The only thing to mind here is the wood inequality between two routes, and whether you are OK with skipping wood in these recipes.

Actually I've being thinking about making a re-balancing for Lignumis' progression recipes some time later. The thing is, planting trees / producing trees with wooden universe is somewhat space inefficient and is not available for all planets, so instead of simply adding wood to original recipes, I think it would be better to replace some of the metal and stone ingredients with wood. How do you think?

Feel free to make a balancing mod. I think there are just some bugs because Lignumis' code evolved while I didn't check AAI compatibility since the initial implementation.