I was lately at a customer where we had some weird behavior so we checked all kind of stuff and realized, that all machines had the same sid. From my perspective this should not be an issue since Mark Russinovich released this article. The only issues persists, if two domain controllers have the same SID.
Then I checked with a couple of colleagues how it is in their environment, that is running smooth – and – all SIDs were the same. So it seems to be standard, that MCS is not changing the SID.
Another issue we found, is that MCS created always full clones on a VMWare based environment. This should only happen in a XenServer environment. The problem is, that the customer only had Terminal Server and not VDI. And MCS in combination with terminal Server images has no choice how the VMs should be deployed. If you look into in Citrix Studio for the powershell command, you can see, that the machines are created as full clone. Saying that it means, that if you want linked clones you cannot use the console but need to use a powershell script.