I was wondering that can Middle Tier Server be a standalone Windows Server
on pure windows 2003 environment, if it can, does it limit some
functionalities etc?

I know that in documentation it says ..

Prerequisites for Installing the ZENworks Middle Tier Server
6.3 ZENworks Middle Tier Server Software Requirements
Windows 2003 )
If connecting to a Windows Server 2003 Desktop Management Server, both
Windows Server 2003 machines must be members of the same Active
Directory domain or a trust relationship must exist between the domains they
belong to.....

I Just wanted make sure has anyone tried the combination with standalone
windows 2003 as middletier server and more that one AD domains (with no
trusts between them) that it will support. There will be one Desktop
Management Server per Domain and those are member servers.

Or has anyone did this with one middletier on linux to support multiple AD
domains with no trusts between AD's?