[NewPM] Fix placement of LoopFlatten

https://reviews.llvm.org/D90402 was inconsistent with where it put
LoopFlatten between the two pass managers. It also missed adding it to
the non-O1 function simplification pipeline.

PR48738

Reviewed By: SjoerdMeijer

Differential Revision: https://reviews.llvm.org/D94650