I did get two libraries in the same package to load correctly in Dynamo Sandbox and Dynamo for Revit.
It did take awhile of tinkering to get it to work. The only way to get it to work was to rename the Dynamo Sandbox library inside of Visual Studio to be first alphabetically. So, for my package Lightning, it had to be renamed Lightning0WA and Lightning1Revit, therefore the Revit library is added second. Note here I used the 0 and 1 (and potentially two in the future) to automatically sort these. This is important because if the Sandbox library, in this case the Lightning0WA, is loaded second after the Revit library, then the both libraries will fail in Sandbox.
Structure in Windows Explorer:
Dynamo for Revit loads both libraries:
Dynamo Sandbox only loads the one library:
Thanks for the nudge in the right direction. Can/Should we add this to the DynamoWiki?