The Grand Masters "perfect" humans were mutations who can handle themselves (so to speak) in the apocalyptic iceage which was prophesied. It was why he stole the mutagens in chapter one, and it is why you fight so many mutants near the end.
Yes, I understand that part; but I assumed the varius pink-colored mutants were the result of failed experiments. I thought the goal of the Bigger Brothers Project (or whatever Siegfried called it) was to create a super-hardy variety of humans/humanoids, not a super-hardy variety of monsters? Come to think of it, the whole ending could be much creepier if Geralt encountered the “perfect mutants” able to communicate. Unfortunately, the end-game mutants are portrayed as regular, run-of-the-mill mute monsters, no better than zombies, so you just slaughter them without a second thought or regret (and even collect alchemical ingredients). That is an easy choice – killing unwitting monsters, as opposed to killing intelligent creatures, "perfect humans" (similar to "non-humans" and witchers). A pity, that might've been awesome, to make that difficult final choice. Remember the talking ghoul in that basement? I spared him though I could kill him. I was given a choice.
Since it was just about killing monsters, the whole “witcher secrets” theft and "mutant creation" aspect of the main plot left me unimpressed.
As for the time travel bits, then it is a classic grandfather type paradox. Or more down to earth - a chicken and egg type situation.
One could speculate that because of The Witcher and training from Triss/Shani (depending on route), Alvin survived to "teleport" back into time to become the Grandmaster. This would mean that if he did not replicate the events, he would not have been pushed back into time, and he would not have been the grandmaster, and .... well, you get the drift.
Yes, but why did Azar Javed want to kill Alvin? Can you explain that? Did he know who really Alvin was? How? If he did know that, he must have known that killing Alvin would undo the Grand Master. Why would Javed want to undo GrMr, his close ally? I don't think it makes any sense. There was absolutely no indication that Javed intended to eliminate any of his associates, whoever that might be, unless I grossly missed something. Besides, what would Javed win by killing Alvin? The only explanation is that Javed knew who Alvin was and just pretended they were going to capture and kill Alvin, so he would teleport back in time (replicating events). That means GrMr trusted Javed implicitly, because he literally placed his life in Javed's hands, which was imprudent on GrMr part. I wouldn’t trust the likes of Azar Javed with my pocket change, let alone my life.
Another puzzle: Geralt was killed by the angry mob, but his body was never found. Who resurrected Geralt and why? The Wild Hunt ghost? What was the “reason” the Lady of the Lake referred to? Was he chosen to fulfill the Prophecy? (see The Short Guide, Part One...

) Or his own Destiny? Btw, I chose not to believe in destiny, but here it is – time travel, the prophesied Ice Age, and whatnot. The free will concept bit the dust.
Where I'm very happy with the ending is that the "end boss" were not impervious and invulnerable to all the abilities you had used in the game and have trained up throughout the hours of gameplay - that is otherwise a common and most annoying mistake in CRPGs in my view.
The GrMr was kinda wimpy. And so was Javed; I expected more from the Fire Mage. He was casting flames in the swamp when he was allegedly “weakened” by water, but forgot to do so in his own laboratory. GrMr surrounded himself with the fire creatures but Javed the Fire Mage failed to produce his fire magic. Actually, I was happy – I hate the super-hard and super-immune bosses too.