Most microcontroller have I2C as second function of a GPIO pin which clarifies that I2C functionality can be covered by a usual GPIO. It's imply done by configuring the GPIO as open drain output. Pull-up resistors are usually added externally, in case of a short I2C bus with low load capacitance, an internal pull-up resistor might be sufficient.
So you mean to say that the internal/external presence of pull-up resistors in I2C will depends completely on the SoC used. The SoCs which do not have this feature, external pull-ups have to be placed and this can drive higher loads.
Well the I2C standard required (dependent of the mode) to have a low-pass filter, the pull-up could be internally or externally.
In our design the GPIO pad has the same functionality as the I2C pad, I means, pull up/down value controllable, low pass filter controllable, Schmitt trigger controllable, drive strength controllable.
Ones a general purpose io pin, whereas the other is a serial bus method of communication. By stating it's an I2C pad the manufacture is telling you...the customer that it meets the I2C standards.
For example I2C standard requires certain properties, "I²C uses only two bidirectional open-drain lines, Serial Data Line (SDA) and Serial Clock Line (SCL), pulled up with resistors. Typical voltages used are +5 V or +3.3 V although systems with other voltages are permitted." - wiki
You'll find gpio pads also are separated into banks that operate at different voltage standards etc.