Not sure how you got to that conclusion, as the pre-commit framework does indeed abstract them away. Maybe you're confusing it with something else?

> hooks shouldn’t be run during a rebase

The pre-commit framework doesn't run hooks during a rebase.

> hooks should be fast and reliable

The pre-commit framework does its best to make hooks faster (by running them in parallel if possible) and more reliable (by allowing the hook author to define an independent environment the hook runs in), however it's of course still important that the hooks themselves are properly implemented. Ultimately that's something the hook author has to solve, not the framework which runs them.

> hooks should never change the index

As I read it the author says hooks shouldn't change the working tree, but the index insteead and that's what the pre-commit framework does if hooks modify files.

Personally I prefer configuring hooks so they just print a diff of what they would've changed and abort the commit, instead of letting them modify files during a commit.