Because Madara had no knowledge of the Yin/Yang Seals. And the Ameno swap damn near sealed Madara and Kaguya within no longer than 5 minutes of the fight. That speaks volumes for how insane that technique is as far as teamwork goes. Not only that, Madara had no way of keeping Naruto separated.
Nafuto have the ability to seal Limbo.
Madara is a sloppy fighter than tends to underestimate his opponents because of his love for fighting.
Well let me explain to you why I think he would win, or at least push it to a degree of difficulty beyond Kaguya. As curtesy to ease his power I'll assume that Limbo cannot use techniques.
To address your first point, Madara after attaining both eyes was going to use the full power of the Rinnegan and refine his fighting abilities after realizing their power and taking them seriously.
Taijutsu:
Madara is superior to both individually. This is shown when Naruto's clones lost to Madara's shadows. With Limbo he is able to completely handle both of them at the same time and overpower each. There's not much else to say here since that information is certain. Clones won't work because Madara has superior chakra and Wood Style clones, which have been specifically stated to be better. Amenotejikara is their best bet but because of Madara's immortality and the recharge it won't provide them a certain win in this category.
Ninjutsu:
Like Kaguya, Madara is able to absorb chakra and most techniques. Any poorly used Rasengan/Rasenshuriken or Chidori becomes useless. He surpasses Sasuke in Fire Style usage and strength. His Sage Art: Storm Style: Light Fang moves at the speed of light and has the ability to cleanly cut through Truth-Seeking Spheres, meaning it should have the ability to pierce through any defense that isn't Naruto and Sasuke's strongest avatars. On the ground, Wood Style creatures and basic usage allows Madara to control the terrain and move through the ground (?). He should be able to use Sage Art: True Several Thousand Hands, but I'll leave that out. You should also take notice that since Madara has mastery over the Rinnegan, he can absorb and cast techniques at the same time, meaning he should be able to use this through Susano'o for some larger techniques. It also becomes useful at other times though.
Limbo:
You started off by saying Naruto can seal Limbo, but that's nearly impossible unless Madara runs off to give them the time. Using Truth-Seeking Spheres wouldn't work because they can simply be removed and if the duo don't continuously watch over the sealed ones, Madara could release the seal and free them. The Databook also states that Limbo has a maximum of four, so it's very possible that sealing them only works until the return since Madara had four when he got his second Rinnegan.
Avatars:
Madara's Perfect Susano'o is stronger than either's avatars but would probably hinder if facing them both at the same time. This is where Limbo comes in handy. We've been shown that one has the power and speed to knock multiple Tailed Beasts near simultaneously hundreds of feet. Keep in mind that this is before gaining the Six Paths Sage Mode, which would provide even more physical strength. With this, the shadows will have the power to knock around Naruto and Sasuke's avatars if not break them at the same time. If Naruto decides to use clones the same could be said for Madara. If they're on the ground the Wood Style creations can also pose danger.
Six Paths Seals:
This is the hardest part for Naruto and Sasuke. They only get one chance. Limbo almost assures that he can't get caught without having all his shadows sealed. Even then, unlike Madara, Sasuke can't tell the difference between clones, so a finely placed Wood Clone would be their worst nightmare.
Ten-Tails:
Madara isn't Kaguya, he hosts her, meaning that he, like Obito, is able to release the ten-tails and fight along side it while retaining his powers. Naruto and Sasuke literally have nothing that can defeat or counter it and it is several times larger than their avatars. I know what you're thinking. That would make it easier for them to seal it, right? Wrong. Because it is separated from Madara it wouldn't affect him at all, wasting their seals. He could either absorb it back, making the Six Paths Planetary Devastation useless or wait for it to finish and resummon the husk and reabsorb the Tailed Beasts.
