the documentation is mentions that Virtual Appliance is responsible for a lot of virtual machines requiring consolidations.
Not sure what you mean, could you provide the quote please?
Why I am really interesting in this is we occasionally have issues with the Snapshot/Consolidation process, either causing phantom snapshots and down the line we encounter stuns on the VMs etc, which is a big issue for us. If I can reduce this even more, I would really be interested.
is supposed to deal with phantom (orphaned) snapshots. If orphaned snapshots appear frequently and cause VMs to stun the I'd suggest you to contact our support team.