No, but they must be in place prior to work starting. This is the sort of collaboration that this initiative was designed to encourage. Provided that the minimum requirement for collaboration is met all eligible proposals will then be considered on the basis of their scientific merit. Ideally a balanced portfolio of projects will be funded. The call for proposals gives an example using the term 'defect'.
Research using disease systems as a model to understand fundamental biology are acceptable.
The significance of the model used should be emphasised. Two main objectives of the initiative were given in the call for proposals but examples were only given for the first. No bias was intended. Yes, if previous collaborations have been on a different topic and the collaboration is bringing together different types of science, as required by the initiative. It would, however, be wise to include a sentence explaining why you have not been able to do this before.