Cook always heavily leans in favor of incumbents, especially early in the cycle. I have never heard of them rating an incumbent as anything worse than Toss Up until at least the opposing nomination has been decided.
I'm not sure what your objection to AZ being a toss-up is. I'd say it's tilt D, so I can't really argue wit Toss Up or Lean D. MT I'd put in basically the same category, and given Cook's bias toward incumbents, I'm not surprised at all they went Lean D.
This map is basically exactly what I expected, except I'm a little surprised they didn't make TX Likely R and PA Likely D.