The insulation at eaves level will leave your loft area comfortable for use and free from condensation. By installing the insulation at rafter level, it keeps the loft void warmer and prevents condensation build-up, which can otherwise occur when increasing insulation at ceiling level. The warmer, drier, cleaner roof space eliminates the risk of pipes and tanks freezing.
I am an Architect in Toronto. I am designing a new roof addition to a row house building. Because of existing conditions and the shape of the new roof. It may be easiest to use closed cell spray foam within the areas of the joists. My question is when spray foam is used in this situation do I need to worry about how the joist members may be thermal bridges? It is not common to provide a little bit of rigid insulation to protect the joist members? The additional layer of outboard insulation will require an extra layer of plywood above the insulation which will add to cost.

If you're chemically sensitive, it's probably not a good idea to get it installed, but it's also not a good idea to breathe musty air from the crawl space either. In addition, your house and its contents are made of lots of materials that affect your indoor air quality. If you're really concerned about this, hire a company to test your air and tell you what you can do about it.