I solved the problem more or less in the meantime.
First, I gave up on the idea of fully automatizing everything.
There are simply too much problem with combining the different bootstrapping repos; anything could happen, really.
One thing I wanted to still automate though, is merging the different dependencies of the bootstrap repos.
So after theese changes, I came up with a really simple script, which usage looks like this: ( Note that gitcopy is a script I use on my linux environment, which copies only the content of a repository. )
gitcopy git@server:bootstrap // Grabs the bootstrap.php file from a private repo.
php bootstrap.php fb-bootstrap api-bootstrap
The second command will create a new folder: 'bootstrap', and clones the repos into it. It then removes the .git folders, since I don't need version control there. It also bootstraps a base composer.json, and merges all the other composer.json files from the bootstaps in it. The bootstrap composer.json files are removed in the process, so I can just copy the bootstrap contents into my project's root folder, without prompts about overwriting other composer.json files.
So basically, it's just a nice little tool to grab everything I need, and after that I can deal with possible problems myself.
With this, I could use Yeoman generators, and still use my own bootstrap files, without worrying about conflicts.
The only thing I couldn't look into, is how to make this script a phar executable, so it could work like composer.
Instead grabbing the bootstrap repo for the bootstrap.php, I could just say: bootstrap api webapp etc
.
But that's for another day. :)