Thank you, Brenden. I'll experiment with a hotfix to see how it handles various changes.
Here's more explanation, in case anyone has additional insight:
Our (The New 42nd Street's) solution contains projects that represent several related, deployable products, including the Kentico web app, a web service, and a couple other apps. The solution also contains projects for shared dependencies, such as a domain layer and helper libraries. In the Solution Explorer, it is arranged like this:
KenticoSite (a solution folder, and a directory in the file structure)
- App (the deployable Kentico web application project)
- Support (a project much like "AppCode")
AnotherKenticoWebApp (another solution folder / corresponding directory)
Namespaces and assembly names intuitively follow the solution arrangement: New42.Domain, New42.KenticoSite.App, New42.SomeWebService, etc.
Past versions of Kentico had opinions about the single CMS web application project. Unlike past versions, Kentico 8 seems to have opinions about the broader solution. For example, Kentico 8 expects there to be three projects (CMSApp, CMSApp_AppCode, CMSApp_MVC) in a "CMS" directory, but at the root of the solution in the Solution Explorer. Now I worry that our preferred solution structure (directory hierarchy, solution folders, namespacing, etc.) will violate Kentico's expectations, such that automatic hotfixes and upgrades will fail.
The worst case scenario would be to have a solution for each Kentico web app and then one for everything else. I'd like to avoid that complexity if possible.