At its core, VSPAERO is a potential flow solver. This means it is incompressible (M=0) and inviscid (Re=inf).
Think about elementary steady potential flow solutions you may be familiar with -- sources and sinks, thin airfoil theory, etc.
In these solutions, Velocity does not matter. You can readily run with Vinf = 1.0 and get the right solution.
At its core, VSPAERO behaves somewhat like this. However, as more complex models are added, things change a bit.
When you add a compressibility correction, you need to add a Mach number. However, as a potential flow solver, there isn't really an energy equation, we just have a compressibility correction. Something like sqrt(1-M^2) applied to the X-coordinate (VSPAERO has two options and they are more complex, but this gives the idea). Consequently, the Mach number is a separate concept from Vinf -- it is just the number plugged into the compressibility correction. We could have you input a speed of sound -- but Minf is what shows up in our equations and people think in terms of Mach -- so it makes sense to have Mach as the input.
Next, we may think about an unsteady flow. Perhaps the wing is pitching in an oscillatory manner -- or there is a rotating blade. Now Vinf matters -- we need to know how far the bulk flow moves in one period of oscillation. This could be described by the Strouhal number, another important dimensionless number of flow. However, people are relatively unfamiliar with Strouhal number -- so it makes more sense to specify the rotor speed in RPM and the freestream Velocity as Vinf.
Most codes use Vinf as Vref -- for airplane problems, this is usually the right choice. However, what do you do for a helicopter in hover or a propeller in a static thrust condition? In these cases, Vinf=0 -- so if you used it to nondimensionalize, you would get a divide by zero. So, we allow the user to specify Vref if they need to.
For most problems, Vref=Vinf is the right choice. However, in some situations you'll want to set Vref separately.
In the case of a fast helicopter rotor -- at a hover condition -- the rotor tips might be at M=0.95. However, Minf=Vinf=0. So, we have MachRef to go along with Vref. That way, we can still apply the compressibility correction to rotating blades in an otherwise static flow.
So, Vinf and Mach should match --- and Vref and MachRef should match.
While you're at it, ReCref should match Vref and cref.
Rob