You're asking the system to install a package. System packages are available to all users. If the package is going to work for all users, its dependencies also need to be available to all users. This naturally leads to what you're seeing: the system will not consider software installed only for your user, so it'll end up installing the same dependency system-wide that you had installed in your home directory. While I understand your frustration, I can't immediately think of a better way to handle this.
