This doesn't cover everything (lumber mill, for instance), but for the purposes of seed generation on Lignumis and Nauvis you can add the following lines of code after line 240 of compat/planets.lua. This will make the burner, steam, and basic assembling machine able to craft seeds:
table.insert(data.raw["assembling-machine"]["burner-assembling-machine"].crafting_categories, "woodworking-or-organic-or-assembling")
table.insert(data.raw["assembling-machine"]["steam-assembling-machine"].crafting_categories, "woodworking-or-organic-or-assembling")
table.insert(data.raw["assembling-machine"]["assembling-machine-1"].crafting_categories, "woodworking-or-organic-or-assembling")
The finished section should look like
if mods["lignumis"] then
table.insert(data.raw["assembling-machine"]["burner-assembling-machine"].crafting_categories, "woodworking-or-organic-or-assembling")
table.insert(data.raw["assembling-machine"]["steam-assembling-machine"].crafting_categories, "woodworking-or-organic-or-assembling")
table.insert(data.raw["assembling-machine"]["assembling-machine-1"].crafting_categories, "woodworking-or-organic-or-assembling")
data.raw.planet["lignumis"].surface_properties.density = 2000
end
It isn't perfect, and does a lot more than just seeds, but if you want to play while waiting for the more correct fix here's a way to do it