There are several differences:
1) The standard modem port has connectors (pins) for signals in and out, timing, and handshaking. The GeoPort adds a ninth pin for power to an external device.
2) The GeoPort also takes advantage of the power of the processor (either the DSP processor in the Macintosh AV computers, or the PowerPC Chip itself) to do telephony- either data, or fax, or even voice. A modem is just a line interface to the telephone wire, a DSP to create the tones used, and software to run it. If we have a DSP on the main logic board, we can build an inexpensive line interface (like a GeoPod Telephone Adapter) and use computer software to run the modem.
That makes it inexpensive to add a modem to a computer, and makes it easy to enhance the modem through software to increase performance, or accommodate a new standard when it becomes available. It also makes it more flexible and adaptable.