Jie,
In most networks different kind of VPNs are deployed gradually based on the demand of customers. Thus it is impossible to make a plan for deployment of all kinds of VPNs at the beginning. And this would also affect the flexibility of deployment of new VPN services.
There is many years of operational experience in deployment of various VPN services today. AFAIK non of the deployments today have found this to be of any practical issue.
I think it would be great at this point to hear from operator's community if they see a recommendation for unique RT assignment for different customers/services as a problem.
Thx, R.