How transfer length of the tendon affects the prestress forces?
The purpose of transfer length is as shown in the image below.
What this feature basically does is just the way how stress is considered at the extreme fibres. It does not affect the axial force of the tendon and the force being transferred to the girder element. This can be verified by checking the beam forces result. The forces would remain unchanged, no matter the transfer length.
Now, tendon primary is the force being applied to the structure due to prestress and Tendon secondary is nothing but the the resistance in the indeterminate structure due to the applied prestress load. Since tendon primary forces itself are not affected, tendon secondary forces also won't be affected.