The free length of the spring doesn't enter into the basic spring rate equation. Only the number of active coils, wire diameter and spring diameter determine the spring rate. Comparisons I have done to measured rates show the calculated value is normally within 10%. Always use measured values when available.

In your case with two identical springs with the free length is slightly different there will be a measureable difference in the spring rate. The taller spring being slightly softer. The difference would be very small.

When using the spring rate calculator make sure you enter the number of "Active Coils". Normally the first and last coils are considered inactive.