Q: In order to prevent the Exchange tool from breaking appts shouldn’t the recommended order be to run Exchange tool, run Exchange CDO, and then patch Client OS?
A: Depending on the gap between the rebase and the OS patch, it could present a gap where appointments and meetings could be created using the old DST rules, requiring rebasing be conducted again. The key point here is to run the client OS update and rebase as close to each other as possible.  the guidance is meant to fit the majority of customers.  If it doesn't exactly fit your environment then there are no hard reasons why you shouldn't do it any which way that works for you.  as long as you are updated and patched and you plan on how to fix meetings with either rebasing tools or manual methods then you are set to go.