You're giving Kabuto a version of Madara he has never demonstrated having (one with no personality, who can't override Edo Tensei). In versus fights you give people their prime power, not power they theoretically could have had. You describe summoning Madara as a "flick of his wrist". That is not accurate. He needs an opening to summon them, which is why he had to back the hell off from Tobi when he was using the tech. This is not Kamui like speed here. Also when he used it on that occassion, none of his summons was activated, and the only time we've seen him summon Madara for battle purposes, we're told by Kabuto "it will take me some time to summon him". So it doesn't seem to be instant for summoning a fully powered Madara at all. It hardly matters though, since a bloodlusted Nagato destroys a village sized area in one shot, which should kill Kabuto instantly (long before he can summon). Nagato requires no seals and has no delay. Advantage Nagato.
No, his Yahiko body needed to... actual Nagato has no such problem. Nor did he need to "soak up alot of Chakra first", he just did it... the consequence was God Pain was weakened after... again, actual Nagato has no such limit we know of, and performs it instantly in the Naruto Edo fight we see (destroying alot of the forrest with his straight on blast), and performing his ultimate move instantly.
Kabuto can't hide underground faster than Nagato can blast him, and even if he can, he can't hide underground and edo at the same time. If they're going in with no knowledge in advance, then Kabuto tries to Edo, and before he finishes he's turned into pavement by a technique he can't even believe the scale of. If they have advanced knowledge, Nagato just aims the blast in front of him, but makes sure it's ripping up a good chunk of the ground too (though even the 360 degree blast creates a crater, and clearly rips up the ground, so I'm not sure how deep underground you think Kabuto can get in the instant it'll take for this to happen... not nearly deep enough is my guess.
You seem to think Kabuto has survived the blast no problems, except Kabuto isn't going to be hundreds of feet away from the point of impact which destroyed a village... he's going to be at the epicenter... he'll be lucky if he's in one piece at the end of that tech, let alone busy forming seals and summoning things... if he does survive, Nagato wll be able to finish him off easily as he lies there badly injured and probably in multiple pieces, probably by summoning the gedo dragon which will finish him before he can do any edo's (and can end the edo's the moment the coffins appear).