MCDUs date back to the first generation FMS that was developed in the late '70s for the B757/B767 aircraft. An equipment Characteristic for the MCDU was developed by ARINC committee and published as ARINC 739. This was replaced by ARINC 739A in the '90s to support additional new features.
The ARINC 739/739A Characteristics do not specify a particular font. The regulatory agencies (e.g., FAA) don't really care as long as it is easily readable and fault tolerant. That last bit is the concern that a dead pixel/row/column in the display causes a character to be misinterpreted.
Starting with the originals, the MCDUs were limited by the technology of the displays. They settled on a 14 line, 24 characters per line (fixed pitch) CRT display. CRT fonts were raster generated. The text layout carries over to the current MCDUs when they switched to LCD displays in the '90s.
The fonts used were limited by the CRT technology and later by the available number of pixels in the LCDs. The constraints of aircraft certification generally means that things don't change unless there's a compelling (think: money) reason to do so. So even with today's high resolution displays, the MCDUs still have a 14 line 24 character layout. With more pixels, the fonts are just higher resolution versions of the older fonts.
In recent discussions concerning displays, the manufacturers want a consistent look within the cockpit, subject to the certification rules. As you found in AC 25-11B, there's some general guidance:
5.4.3 The choice of font also affects readability. The following guidelines apply:
18.104.22.168 To facilitate readability, the font chosen should be compatible with the display technology. For example, serif fonts may
become distorted on some low pixel resolution displays. However, on
displays where serif fonts have been found acceptable, they have been
found to be useful for depicting full sentences or larger text
22.214.171.124 Sans serif fonts (for example, Futura or Helvetica) are recommended for displays viewed under extreme lighting conditions.
In my experience, Futura seems to be the most commonly preferred but others do come up. Not surprisingly, some fonts are copyrighted and are subject to licensing fees which reduces their popularity.