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Help Understanding RTC Hardware

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So I noticed that games with RTC (such as Pokemon), the RTC IC (S3511 - 8pin RTC with 3-wire serial bus) is connected to the GPIO pins of the ROM chip.

Does anyone know, are the GPIO pins set as input only? Meaning it can only read the data on the RTC IC? Is it able to write to it?

As far as I know, for pokemon it detects how much time has passed by comparing the data stored in the S3511 chip with the the data stored on the FRAM for the game save. It then compares the two to see how much time has passed.

I believe there are homebrew programs that changes the date. But as far as I know that's within the game save only and not on the S3511 chip?

What exactly is the chip that stores the ROM? I thought it was just flash memory. But it appears to be flash memory device that is capable of three wire SPI to write a portion of memory to the flash to read RTC, and also has a parallel interface to read the data stored on it. Is there a similar device that is commercially available?

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