All sites on our Cloud platform get treated as completely separate entities by Google. There is no disadvantage, even if you run thousands of websites through us (and some customers do!).
Even though you and we know that your websites are on one platform, there's nothing to the outside world that shows that they are linked. One website will not link to another.
On the Cloud, in fact, the codebases are completely separate. PHP runs under a different user, the storage is probably separate, and it'll almost always be served from different web servers and database servers too!