Had this same issue. Had to add this in data-final-fixes.lua to resync after space age additions.
local chem = data.raw["assembling-machine"]["chemical-plant"]
if chem then
local existing = {}
for _, cat in pairs(plant.crafting_categories) do
existing[cat] = true
end
for _, cat in pairs(chem.crafting_categories) do
if not existing[cat] then
table.insert(plant.crafting_categories, cat)
end
end
end