Currently playing 'Enable All Planet Mods' (with some additional qol mods) now, and have unlocked lumber mill productivity upgrade, making it total 75% productivity bonus.
And I recently found that recipes only in 'intermediate product' category have 75% bonus, while other recipes (like wood ammo or lumber mill itself) still have 50% bonus (which is default lumber mill bonus).
I wonder this is intentional setting or not, or have I missed something?

This is a side effect of how MUpgrades gives prod equivalent to how a prod module would give productivity. A recipe can either allow productivity from modules (including MUpgrades, which uses hidden beacons) or it can't. This is an engine limitation that I cannot fix, unfortunately.