Then OP would have said 'Madara vs. Kakashi ... Restrictions: Kamui, EMS, MS & Mokuton'. Instead he wrote 3T Madara. He's referring to pre-MS Madara.
As I said, he is able to use only 3 Tomoes Sharingan now as well. 3 Tomoe Madara doesn't hint us to a moment in time, but to a fighting way. For example, if he said Edo Madara we would have know that only the feats in this war arc are the ones he means, but since he didn't mention it, it doesn't count. As I said, 3 Tomoe Madara can be even before his death.
And if you're really that unhappy with Mokuton, fine. See the taijutsu in the Madara vs Shinobi Alliance fight, 1 vs 1000. Kakashi has an implanted Sharingan in only one eye, Madara is a pure Uchiha with both eyes awakened normally, he'd beat Kakashi easily. Then there's Katon in which Madara shitstomps Kakashi.