I'm developing a modular game in Unity 5.6. Each module has very little overlap in assets with the others. I'm concerned about having a bloated repository after a few months of development, and since I'm using Bitbucket (a free account) I'm limited in my repo size, but not in my number of repos. So instead of having one huge folder for my game I'm considering having a launcher project and scene that loads builds from a folder in /Assets. Each module would be its own project, and I would just drop its build into the launcher's folder.
My question is, is this a reasonable approach to building a highly modular game? Hopefully I'll be continuing development for quite a while, and I want to make sure the project is as lightweight and extendable as possible. Or am I overthinking this, and should I just use one big repo?