If you want a dedicated Org vDC Per User/Project, you need an Organization Per User/Project then.
If you have multiple users per Org, the will have access to deploy to any Org vDC you have given to an Org.
I think you might be able to get around this with Quotas. Each Org vDC could have a quota equal to the number of required VMs (if it's very explicit).
then each user could have a running VM quota equal to the same.
then each user could make a vApp of the required size, and each Org vDC could only support a single instance of that specific size.
that's a really wonky workaround, but might help.