Madara was restricted but i guess that's how story goes, you can't keep everything up to the standards. Madara only used mokuton against gokages even then on a restricted scale but used his PS. against hashirama again he didn't show any mokuton heck when he was bound by wood dragon, he should have been able to counter that with his own mokuton. As alive again no mokuton. So madara against gokages seemed more threatning because he showed variety of techniques. He didn't show any technique whatsoever as jubi jin either. I know he showed CT n all but that was nothing worth mentioning.