I have made a test VCA project for your testing. It actually seems to work very well. I have all vcas in a top level VCAs folder and all slaves control audio tracks, not folder tracks. In my case I have a Vox folder, VoxLd for lead vocals, VoxBg for background vocals, I put a delay on the Celine vocal in VoxLd and I put a distortion on VoxBg track Girls.
The Master Slaves Groups are as follows
Master
VCAs VCAs
Vox Vox
VoxLd VoxLd
VoxBg VoxBg
Then the tracks are Slaves like this:
Celine Slave to VCAs, Vox, VoxLd
Girls Slave to VCAs, Vox, VoxBg
Sample test project for Reaper 5. Click the DL icon on top of this page:
http://www.sunriverstudios.com/temp/test1.zip
This seems to allow automation on any of them to control appropriately and as expected. Let me know if I'm missing something.
Let me know what you think !