There are not separate pullups for those pins. The Wire library enables the internal pullups, but I don't think it will be invoked unless you call Wire.begin().
When you write LOW to a pin configured as an input, you are just turning off the internal pullups. The pin is floating, not pulled down to ground.
Normally you enable the pull-up resistors to hold the line HIGH when not connected or otherwise driven, and your interrupt drives the line LOW when asserted.