The Content Transfer Tool doesn't require (or care) that your source and destination are in the same org, as that's not at all how they authenticate. A primary use case for the CTT (and how I've used it in almost every case) is to transfer from an on-prem 6.5 environment to AEM as a Cloud Service, and in such case the source environment is not in any Adobe-managed org at all. In fact, the last time I used this was done on a copy of a 6.5 Author that I had hosted on a computer under my desk.
So, the answer to your question is yes - you absolutely can migrate content from two separate orgs.