First off, that document is as old as I am.
Second, I used to work for the ETS group at NOAO in downtown Tucson (on the University of Arizona campus), and at the time, we used Accel for schematic capture and layout, and that schematic capture required junction dots to indicate wire connections.
Third, that document does have a lot of anachronisms. For example, it wants to have capacitance shown in picofarads and microfarads, which are fine, except that nanofarards are a better choice for many common values. (100 nF or 0.1 uF? I vote: don't use that decimal point, as it might vanish on reproduction.)
Further in that document, say on page 23, I see a capacitor with value "4700." 4700 F? That's a big cap. See what I mean about being explicit? The reader, 51 years later, shouldn't have to guess what was meant by something on the schematic.
I remind you that you originally said,
and you use a 50-year-old standard to illustrate your point. Maybe by "modern" you mean the Mid-Century Modern architecture and decoration style that's so popular around here?
All of that is, of course, completely beside the point, which was made earlier: software cannot be ambiguous about this. It wants the user to make intentions clear so it does what is expected.
In fact, in the EAGLE document to which you link, "Pro Tip #1" is "Clearly Show How Your Wires Connect," where we read:
One can complain about many of Kicad's usability quirks, but its use of the industry-standard dot to indicate wire junctions is not one of them.