Because there are so many possibilities, it is very difficult for engines to see through openings.
Why is 1.Nf3 is the top engine move?
@1
It depends on the engine. Stockfish prefers 1 Nf3 now. AlphaZero 1 d4. The engines that the top GMs use 1 e4. Also 1 c4. The 4 moves are equally good. Chess is a draw.

We have to presume that there is an opening starting with Nf3 which it evaluates as strongest for White which can't also be forced to transpose into another opening by Black.
I'd expect that this opening evaluates as strongest by a small margin due to a quirk of the pruning and/or the scoring system used to evaluate a static position. You would find that as you traced through to that position the evaluation changes and it doesn't actually give the strongest possible position for White but the limitation placed on the evaluation by the search depth leads there.
The topic name speaks for itself.