No, the number of check-in/check-out has no influence on the price billed.
FAIRTIQ automatically computes the price at the end of the day, depending on all the trips taken. The system might group two tickets into one if the price is lower.
FAIRTIQ must always be active when you are onboard a vehicle.
If you are connecting between train/bus, we recommend keeping FAIRTIQ active (max 25-30 minutes).