That GPIO is driven by the low power microcontroller inside the module. That microcontroller is connected via i2c to the modem. The not connected message occurs because the microcontroller is asleep when it receives an i2c message to change the GPIO. The microcontroller then wakes up and the master retries the i2c command and it succeeds. I don’t remember the exact timing, but I recall that the microcontroller goes to low power mode after a couple hundred ms.
So to eliminate the message you would have to find the code that generates the log message in the i2c master driver and remove it.