If you mean the “Did You know?” tips, those are just general information. Disabling Vsync doesn’t affect the desktop viewer. It’s also not strictly required for games usually BTW, in 99% percent of cases vorpX bypasses VSync regardless whether it’s on or off. The hint is pretty much just meant for the remaining 1% where that may fail.
The desktop viewer is quite different from vorpX game profiles. It can still do some things like e.g. mouse based head tracking etc, but a lot of other things (most prominently stereo 3D), don’t work with the desktop viewer.
In general always try to run games with vorpX hooked. The desktop viewer is great for doing desktop tasks, but for games hooking the game is always better, even without 3D.