When to hire a Commissioning Agent

I think you will be fine with this plan. It is good to make sure that the method your CxA uses to for items from the review shows dates and resolutions prior to bidding (or frankly even after award if it needed more research) would demonstrate the intent of the credit. Later in my experience, we would use one master Action Item list. We did not like a "deficiency" or Issues Log or other terms that seemed to indicate errors or problems should be the only thing listed. By using the term Action Item, we included all sorts of things that needed to be investigated, reviewed, evaluated, researched, etc. They did not have to be problems or issues.

We are working on a small, major renovation/new construction project where some disciplines, including MEP, are a phase behind the Architecture. (Existing building = surprises that delay parts of the schedule.) We've advised the team to get CX review before bid to comply with the requirement of design phase review. For the comment above, "review shows dates and resolutions prior to bidding, ... or even after...", is there any guidance regarding whether the commissioning review itself might be done based on the Bid Set, vs an earlier CD Phase Set? The owner is on board to have any changes made via Addendum, and would prefer not to pause the bid schedule for CX review to occur. Any thoughts on whether it's acceptable (although not ideal) for the CX review to happen on the Bid Set? 

I also prefer "Actions" vs "Issues" terminology, thanks for that tip!

Are there any updates on this?  Has this approach been accepted by LEED review teams?  We have a similar situation on a project right now.