How does my ic card know which train i took?

I am sorry if this is a stupid question but I just cant wrap my head around it.
Navitime states that when i want to go from Narita Airport Terminal 1 to Sengakuji directly i can either take the "Keisei Narita Skyaccess" or the "Keisei Main Line".
In contrast to the "Skyliner" both of those can be paid with just using a IC-Card no additional ticket needed.
So if I understand this correctly i just touch the IC-Card-Reader when entering the station at the Airport and then again when leaving "Sengakuji" Station, but Navitime says "Skyaccess Line" costs 1466 Yen but the "Keisei Main Line" just costs 1271 Yen when using an IC-Card, but how can my ic card know which of those two trains I took to debit the right amount?

Because there is an other/ additional turnstile to go through

The Main Line trains use a separate section of the platform than the other trains, which is accessible only through an additional or separate set of ticket gates. Best question of the year!

Your IC card knows which route you have taken, not train.

Narita Airport Station (Keisei, in NRT T1) has double gates,
(so does the station in NRT T2,)
for the fare collection system to specify your route.

The Keisei Main Line tracks are inside the inner gate, in a separate zone.
At the inner gate,
your IC card receives a record of your getting into or outside this zone.

The system can judge which of the two routes
by whether your IC card has such a record marked at the inner gate.

When logically there are plural possible routes of different fares,
the system chooses the lowest amount.

In my previous reply:
different fares -->> different amount fares