I am a systems administrator myself, so I have had lots of experience with this. Most settings are stored in the 'AppData' folder, which is moved when accounts are transferred, so all settings from Firefox, Chrome, SnagIT, Cute PDF etc. should be moved over with no problem. Secondly, all of their documents on their desktop or in my documents will be moved over automatically. The only problem you may face is that wallpapers and settings like font sizes and resolution will not be moved over, so your users will have to set these up manually.
You are correct in saying that having a domain with TS does give you many more settings to restrict user behaviors, like changing wallpaper and installing programs.
Let me know if you have any more questions, I am happy to help!
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