When you run the program in this mode, the following window appears and if you watch it closely you will see that the above relationships hold.
Now the eccentricity of Venus' orbit (effectivelky the epicycle) is 0.7% while the eccentricity of the Earth's orbit (the deferent) is 1.6%. Ptolemy assumed that all epicycles were circular and only applied offsets and equants to the main deferent.
Try adding a 3.2% offset to the deferent. Alternatively try a 1.6% offset plus equant. Is the latter significantl;y better?
It is worth pointing out that the maximum angular discrepancy always ocurs when Venus is passing right in front of the Sun - during which time it is impossible to observe anyway.