How does the PM or Fountas and Pinnell (F&P) benchmark fit into the Science of Reading. What can you do instead?

It doesn't fit! If you follow the Science of Reading and the Simple View of Reading model, then you wouldn't and shouldn't be using these assessments. The PM/F&P limits students as it doesn't allow for students who don't have schema for a particular topic (See Dan Willingham). It also assesses a reading model that is not evidence based. Unfortunately, PM benchmarking is a very common assessment tool still used...