Naruto and Sasuke win last three scenarios, loses first. The last scenario can go either way, but I'm still leaning towards Naruto and Sasuke.
- Continuous Senjutsu enhanced Bijuudama and PS slashes can and will destroy any Mokuton constructs bar SS, even if Madara coated Mokujin. Flower Tree World is countered via Enton Rasenshuriken, especially considering Sasuke is capable of seeing it's chakra.
Myojinmon is hardly going to make a difference, Naruto can dispel his avatar partially and keep going.
- SS is eradicated by a giant Flash Bijuudama and repeated PS slashes(that are above Madara's own), the Bijuudama will be on a different level from before, considering Naruto can focus his Senjutsu chakra, and is cooperative with Kurama.
- Madara's lone PS is getting shat on by Naruto and Sasuke's fusion, not only do they have superior durability, they also have far superior firepower. Sasuke's cloaked PS is beyond Madara's, let alone being fused with BSM avatar.
Overall, Naruto and Sasuke have many counters and versatility. Ranging from Sasuke's summons, Enton usage and superior Kenjutsu to Naruto's own summons, clone usage, Rasengan variants and CQC capabilities (chakra arms, Frog Kata, SM attributes and so on.)