Can anyone clear up the transfer from conventional line to Shinkansen line and then getting on conventional line situation again.

https://smart-ex.jp/en/entraining/ticket/

I am basing this off the using IC card for conventional line part. Heres my understanding.

Step 1: I tap IC card to enter conventional line.

Step 2: I use the conventional line to get to a shinkansen station and thus I tap it at the exit gate for conventional line and head to shinakansen gate and that deducts the fare from IC card for conventional line.

Step 3: Dunno why I have to tap the IC card here again if I have the base and express fare for shinkansen as tickets.

Step 4: Exit shinkansen gate with the 2 shinkansen tickets and tap IC card to enter the conventional line and exit at final station.

Now step 3 and step 4 would make sense if the shinkansen gates acted as exit and entry for conventional line respectively.

Really confused about this.