Why not Bxa6 in this position?

I thought being up a pawn up with the resulting position would be better, why does Stockfish disagree?

Well, what does it say? Presumably that offers a clue.

It says you won't hold on to that pawn.

Says not to take the pawn on b7, that is why am asking. I don't see the reason. Why bxa3 instead?

Look at the two end results, one has an extra pawn, the other doesn't. But the one without the extra evaluates it as better for white. Why?

Black has the move in the one with the extra pawn for white. Black's light squared bishop is already developed, although it is blocked by its own pawn.

Because 1. You give up the Bishop pair. 2. You open a file for blacks rook 3. You don’t win a pawn, blacks Bxa3 is horrible.

In post 3 white is better because of the control over b8. 

As for the initial position at the end of the line must be to do with king safety. And if black gets c5 at the right moment those pawns become weak.

 - Trading a good bishop for a bad knight.

 - In your final position your extra pawn on a2 is part of a doubled-isolated pair of rook pawns, basically worthless.

At least when we're talking about pawns, winning material isn't really the point of the opening phase, as crazy as that might sound. Mostly focus on staking some claim in the center, making your knights and bishops active, and castling the king to safety, otherwise it's often the case that the player who is ahead a pawn or two has the worse position because they're behind in development.

https://www.chess.com/article/view/the-principles-of-the-opening

1st line: you have extra pawn, and black is TO MOVE, pawn which is completely worthless as people already say

2nd line: you do not have extra pawn, but it is your side TO MOVE, black bishoop undeveloped and if black wants to make Ba6, there is a pawn (worthless one!) which has to play, so one completely useless move (a6-a5) to make just to enable proper development of Bc8.