Sorry for the late answer, but I needed something similar: I needed to put together tool applications in a portal.
I found a way to include child applications in a parent's Compound application as node modules. I wrote a guide on how to do it and sent a pull request to add it in the advanced folder of CompoundJS' guides. It is also available here. It requires a bit of work, but it works fine with 4 applications for us.
Hope it can help.