The thing about fire walls is that their use is limited to the purposes of "determining area limitations, height limitations, and type of construction" for each portion of a building divided by fire walls. A fire wall is also permitted for creating separate buildings on separate lots as a party wall (no openings). For all other code applications, a fire-wall-separated building is still a single building.
That said, a fire wall could create two R-3 units for determining allowable area and height. However, as someone previously mentioned, why would you want to do that? If they are three connected dwelling units, each with its own entrance located at grade with no units on top, why not consider them townhouses and use the IRC? Thus, you can avoid the more restrictive fire wall separation of the IBC to use the separation wall requirements of the IRC.