This is a holdover from the old HOST computer system that was installed in all enroute air traffic control facilities (ARTCC's) in the mid-70's. The original code was written in just 16MB of RAM. All flight plan processing is done by the enroute computers.
Although the mainframes were updated twice before being replaced in the mid-2010's by ERAM (EnRoute Automation Modernization) the same core programming remained until ERAM.
The old HOST system stored fixes in and adjacent to the ARTCC airspace. Distant fixes were not generally stored. If you filed AAA-BBB and they were so distant the enroute computer didn't know the location of both airports (or fixes) it couldn't process the flight plan, requiring manual intervention by the controller to insert lat/longs to tell the computer where things are. That was the reason for one fix per ARTCC. The fixes were close enough for HOST to know their location.
In ERAM, that problem doesn't exist. ERAM knows all fixes in the US, and many internationally. If you file KJFK..KLAX, ERAM will process the flight plan without error. It will also apply adapted departure routes and adapted arrival routes, which means that you probably won't get that direct non-stop routing that you requested between two busy international airports.
I can't tell you to ignore the AIM, but if you do file direct, I don't think anyone will say anything about it.