Re: LOL Well its canon now. Logic is offically dead.
I think people are exagerating and we need to give Kishi time. We've called loopholes that get cleared up later, often by the next chapter or two from people *****ing.
First off, all Itachi said is that the Mangekyo AWAKENED a third power WITHIN him. Never that you specifically need to have the eyes to continue to use the technique. Remember the brain is what triggers changes to the eyes for the Uchiha and the Susanoo is a manifestation of their hatred so it could just as well actually be manifesting from their brain. This does not explain why a single Mangekyo user like Obito doesn't use Susanoo though, but we can add that Madara is a Yin-Yang user now so his ability to manifest things is greatly expanded now.
As for Madara taking these blows...A big part of the chapter was giving Gaara some screen time. It's a pattern where the good guys kick ass for a chapter, then the villain gets the upper hand. Remember Madara was using his Susanoo which is considered a better defense than Gaara's sand. His armor took the brunt of the tails and he still lost an arm which would pretty much be an auto-lose (Jiraiya) for most people but Madara has help. In reality it was a devastating blow but Madara keeps getting lucky with things happening at the right moment.
As for the eye pop...Remember he absorbed Hashirama's Senjutsu so he must also have his healing factor. This probably lets him pop in his appendages/eyes in place and auto-heal around it so no need for surgery downtime. Remember that Hashirama's cells are like Armstrong in Metal Gear: Nanomachines, son!