I know the thread which says that rebase is for small changes of teamMates, while merge for large changes.
I keep three Gits of three teammates in the following dire
The fact that they are not inside the same git as you state doesn't limit you in any way. Git is distributed, which means that you can fetch between those repositories, merge, rebase, and so on.
Look at git remote --help to see how you can name your teammates repositories in yours so that you can easily import their changes, rebase onto them or perform merges. There is no need to change your directory structure, yours is perfectly usable.