Total fare is not charged for the entire journey. There are some discounts.
As per your example, the fare charges were:
1) HWH to MAS CC fare (Without Safety/Development Surcharge)
PLUS
2) HWH to KPD...
more... 3AC fare (Without Safety/Development Surcharge)
TOTAL MINUS
3) HWH to KPD CC fare (Without Safety/Development Surcharge)
The base fare are calculated first and after reaching step 3, development charges/superfast charges/reservation charges and all other related are added to the same.