So next, without going full-barrel MultiCore, I am hoping that I can use BaseModule as a way to compartmentalize Proxies, Commands, and by extension Mediators and their view components.
Please resist the urge to do this. You will simply be trading one undesirable architecture for another. The existing architecture is burgeoning, but still following best practices. The new architecture you propose will leave you with spaghetti. Lots of things were tried before If you're going to go modular, use MultiCore. Think of those who inherit the application, particularly if it's you.
1) Make a refactor to MultiCore a '2.0 priority', and proceed with best practices for the Standard version
2) Step away from the project for a day or two, do study MultiCore and the available demos, posts and articles and then proceed with an orderly refactor to MultiCore.
Number 1 is what to do if you really can't spare the time or you know for a fact that the refactor would take too long.
Number 2 would be a speedbump, but if you are chugging along fine with Standard, I guarantee you that MultiCore will not be that difficult to understand, the challenge is in coming up with your modular architecture, a simple module loading and caching mechanism (hint: Mediator is a good place to start) and decide if you want to make your modules talk to each other.
I gather that you just want to 'snap in' a UI and the attendant PureMVC classes when needed. So that sounds like you might not have much intermodule communication, so probably interfaces are best for you to get going).
There is the pipes utility if there will be lots more routes than just from the child to the parent and back. There are interfaces where the parent and/or child have references to each other and communicate via interface methods. The big problem people run into is timing and protocol. Being sure a module is loaded before sending it a message (hint poke in and out pipes into it and listen for an 'i'm listening' message before sending anything).
There is also LICS, a new approach to doing MultiCore that's meant to be easier than pipes, but I've not investigated it. And there is Fabrication, which is probably a bit more of a bump than you want to hit this week, but offers a lot of functionality for intermodule communications.