I can see in the log that one of the pools is taking some 30 seconds to mount. This isn't a big deal, but I can't reproduce this, and it should not do that. In fact, there is code in covefs that facilitates signaling among pools in order to prevent this.
I've set up a similar pool structure, 2 pools, each containing 2 physical drives, and then one root pool over those 2 pools.
So like this:
I then rebooted and in my case, all 3 pools mounted at the same time.
From my log:
DrivePool.Service.exe Information 0 [Main] Starting CoveFs... 2017-11-16 08:05:55Z 176067593
DrivePool.Service.exe Information 0 [CoveFs] Pool found on: \\?\GLOBALROOT\Device\HarddiskVolume11 (pool ID=ff8e822d-e0e4-43c9-be67-11b6382f5b1a) 2017-11-16 08:05:55Z 176251462
DrivePool.Service.exe Information 0 [CoveFs] Pool found on: \\?\GLOBALROOT\Device\HarddiskVolume9 (pool ID=bc7aa180-b4eb-4bc5-b1de-4b53fa14c47c) 2017-11-16 08:05:55Z 176253372
DrivePool.Service.exe Information 0 [CoveFs] Pool found on: \\?\GLOBALROOT\Device\HarddiskVolume13 (pool ID=87d2ad52-8fd2-4d44-ae8b-0bfe8be01a3f) 2017-11-16 08:05:55Z 176254744
DrivePool.Service.exe Information 0 [CoveFs] All 3 pools mounted. 2017-11-16 08:05:55Z 176276863
So I'm not sure what's going on there.
If you can, try to get a proper boot log, the one posted on the forum is not complete.
VDS should not be involved in pool mounting. VDS might delay a service startup, but pools mount completely independently from the service (when CloudDrive is not concerned). Covefs and Windows PnP control pool mounting.