OK it's 6 months late, but at least you got a reply
Re 1 & 2:
The problem essentially occurs because we gave no thought to multiple projects that were part of the same namespace hierarchy. In the short term there is nothing for it but to live with the fact that your model is comprised of duplicate packages for ancestor namespaces eg.
We have discussed the matter at Sparx and concluded that perhaps you should be allowed to connect to a Solution as well as a VS Project (just as an Eclipse package might connect to a workspace rather than a project). This idea seems feasible and we are looking at implementing it some time in the future.
Regarding question 3 - the answer is no. Each workstation needs to be set up to connect to the individual projects.
Regards,
Phil Bachmann
Sparx Systems