Moserw,
The first tip you may want to follow when comparing two SDC files is to do the two different Timing Analyses with the same fit (same place and route result). This ensures your timing is constant and therefore you can do an apples to apples comparison. If you believe the SDC files are equivalent, then you should get the same exact slack (note you may need to look at multiple paths to confirm all paths are the same).
In your simplistic example, there is really no advantage of using a virtual clock unless you also use clock_latency to model the delay from the clock to the clock pin. Virtual clocks are also useful when you want a way to easily add multicycle or false path exceptions on the I/O paths (because it is easy to make an exception from the virtual clock to the clock).
Anyway, do the two analyses and see if you can confirm your slack is the same.
David