This is standard for any airline

When checking in excess baggage, fees are calculated based on the journey being undertaken at the time

Since you were stopping over in Dubai , you were originally charged excess fees based on Texas-Dubai . When checking in at Dubai, you were charged Dubai-Jakata

If you had had no stopover, then you would have been charged the excess fees for Texas-Jakarta

Cathay would work in exactly the same way; if you have not been charged, that is an exception to the rules

When you purchased the ticket , you were provided with a baggage allowance; being in 1st class , you received the 1st class allowance; that you went over that allowance, then need to be prepared to pay the excess fees