hubertmroz We are not aware of some sort of long term problem with running the cleanup script. By all means, though, shutdown the last server first and give yourself some time to understand if this form of management will work for you. There is nothing that says that you need to clean up as soon as the last server is shut down. I would encourage anyone to make really sure that this new management paradigm will work for them before they make changes to Active Directory.
As far as complex AD topology - at this time I'd suggest to not jump into the PowerShell only management for this; I do not think that we have a full idea of how multi-domain scenarios work, especially with multi tenant connectivity.
mdicha I hear you... at this time we do not have anything to announce on this, but that is indeed the best care scenario that we want to get to at some point. But nothing to announce / share on that.
Martijn_Westera As mentioned in a previous comment - this will depend on if this is a DAG or just two servers (for redundancy). If just two servers, you could just shut down both and test with new management tools package without removing anything. If the new tools work for the organization, I'd suggest uninstalling one of those servers then (both should be up when you do that) and then shutting down the last server. Once that is also seen as working properly, then you could "clean up". Note that the management tools can also be installed on multiple workstations.