Why are some of my modules reporting missing inter-module dependencies after migration?
Are those missing modules in your sites/all/modules folder? I'm not sure why they would have been left out of a file migration, but anything's possible. 

Modules do not 'create' other modules (except possibly Features, I haven't used that in awhile) in the sense that you're referring to w/ the cTools example, though there are modules that exist as part of the parent module package.