After some trial and error, I was able to create a project with the EnderIO source code that compiled and debugged successfully within the IDE. EnderIO can optionally integrate with some mods at runtime if they are present (e.g. NEI and Waila) and it would be nice if one could define custom debug/run configurations that use a subset of the mods at launch.
This would be useful when developing/testing mods with optional dependencies (i.e., watch behavior with and without Waila loaded).
Also, it could speed up the edit/compile/run cycle of development by not having to wait for forge to load optional dependencies while working on the core features of the mod (i.e., your mod can optionally integrate with ExampleCraft, and ExampleCraft adds an additional two minutes to the startup time).
I did discover that the list of jars that are passed to Minecraft when debugging are passed to the DebugHost through the CLASSPATH environment variable, and the string value derived for the CLASSPATH directly comes from the project references:
https://github.com/tunnelvisionlabs/JavaForVS/blob/00cebbfdef2ea764b031045426e16376d40e34ca/Tvl.VisualStudio.Language.Java/Project/JavaProjectConfig.cs#L214
So a work-a-round for now is to manually remove the reference before launching (it can be added back with the provisioning command).