As you stated, when the Macintosh receives TCP/IP packets encapsulated within AppleTalk packets, two steps are taken. The first is the stripping of the AppleTalk information and the passing of the enclosed data to the appropriate communications application or driver.
The second step is the interpretation of the TCP/IP packets by the receiving program. If you are using MacTCP, it handles the TCP/IP information in the same way that the AppleTalk drivers handle the AppleTalk information. If you are using an application that is not using MacTCP, like NCSA Telnet, then the application is responsible for providing the same functionality as that provided by MacTCP.
A GatorBox or similar device acts as a higher-level gateway. It translates NFS (Network File System) protocols into AFP (AppleTalk Filing Protocol) and presents it to a Macintosh. The Macintosh "sees" an AppleShare server and sends AFP requests to that server. These AFP requests are translated into NFS requests by the GatorBox software and are then sent to the host.