Why did Satoshi not choose for Segwit?
Satoshi made many design decisions that are now criticized (like signatures in transactions, 2-week difficulty period, halvings, etc..). He also made some maths error in the whitepaper. Satoshi wasn't a perfect designer and his C++ code was not up to the highest standards.

We will maybe never know for sure why he chose what he chose, but I'd personally argue it was for simplicity sake.

On a more tangent note: while SegWit looks simple on paper (just put the signatures on the side), in practice, it's quite a complex change to implement. It took months for the most experienced developers to review it.