Having all the code in one directory I half understand, but I actually think the real question a project needs to work out is whether they are going to build up an internal repository of packages to share across projects or not. I don't think you should mix share packages and non-shared packages (with different GIT management rules) in the one directory. I actually think that would be more confusing. So my rule is "app/code" is for code for that project alone (no sharing), "vendor" is for composer shared packages. You can then .gitignore the vendor directory.
