When I saw this thread I thought it was a joke as I don't import VM's from vCenter directly into vApp Templates so I never ran across this issue. I had to check it out to see you are correct.
My process adds a couple steps but it can be automated via PowerCLI or VCO as well.
The way I do it is:
- Create a new vApp
- Import any number of VM's from vCenter that you want to be a part of the vApp
- Capture to Catalog
- Test deploying from it
- Delete Test vApp and original vApp
- Consolidate vApp Template disks (if Fast Provisioning is enabled).
I've done this with 2,3, and 4 VM vApps.
Eric