You mention two different issues here:

1) The usage of the pressure load factor.

You are right, if the factor is set to 1 during calculation of SIX and SIF, the results become safer / more conservative.

This is actually done when using the NEN 3650 calculation option (not available in the educational version).

When calculating "general", we decided to apply the pressure load factor as we feel that the results would be too conservative otherwise.

2) Calculation of the K, SIX and SIF factors.

The calculation differs when using the NEN option or the General option.

In case of a NEN calculation the formula's you mention are used.

In case of a general calculation more complex formula's based on Clark & Reissner-ASME/TNO) are used:

This explains the differences between your manual calculations and the results in Ple4Win.