How does the commuter pass know which way I took on the yamanote/chuo sobu


I got commuter pass from Ikebukuro to the purple dot. I transfer at shinjuku, but since both yamanote and chuo-sobu are jr I don’t tap through and gates at shinjuku.
However, in this scenario, I wanna travel to the designated goal where the red dart is at. Since I am a cheapsteak, I wanna use my commuter route (which is longer) but there is no way for the ic card to know I took the route I drew, rather than the faster route which google maps wanna take. Do I need to tap out and in at shinjuku to prove the route I took? Or how does it really work?
Tha ks in advance!

by Ero__Sennin_

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