In-place upgrade Windows 2012 r2 to 2016 questions.
i would recommand that you are do it in a Test System with 2-3 Added Devices when you try an Upgrade Process.
If you set up a new Server and move the Scanners to the new one you must set up the new Server completly New.
And for the Device moving (from server 1 to Server 2) you may need the Porfessional Service .....
What Devices do you have?
Windows Classic or WM/CE , Android and Apple
You can use MS SQL 2016 SP2 Express for MobiControl v15.2.0.
Out of the 2 approaches you mentioned, the in-place upgrade of Windows Server and SQL Server (Express Edtion) should be comparatively easier. However, there is always risk of breaking the system in either approach if something undesirable is performed in the process. Making VM snapshot and full back-up at each stage of your in-place upgrade should help to avoid problem and allow possible fallback.