This answer is targeted at the title of the question, not to the specific problems of the question in detail.
I ended up using this solution in my project, which allows me to use the custom bootstrap classpath selectively, by activating a maven profile. I strongly recommend using a profile for this, because otherwise it makes the build fail for anyone that does not have the environment variable set (very bad, especially for an open source project).
I only activate this profile in my IDE for the "Clean & Build" action.