The earliest references to "Macintosh System Software" are in the Read Me documents on the System 4.0 Finder 5.4 and System 4.1 Finder 5.5 disks. The first named and numbered release was Macintosh System Software 5.0 (System 4.2 Finder 6.0). For more details on these developments, see my notes on Macintosh software releases.
The misleading "System Software" numbers used in Apple Knowledge Base article 15582 for earlier releases appear to be based on a CD that came bundled with the second issue (April 1990) of Apple's old quarterly technical journal, develop. The CD includes disk images for early "System" versions numbered 0.1, 0.3, 0.5, 0.7, 1.0, 1.1, 2.0, and 2.0.1.* Unfortunately, the disk images on the CD are a jumble of omission and repetition. These mistakes have been passed along as recently as the Apple Legacy Recovery CD (May 1998), which includes disk images for early "System" versions numbered "System 1.0" and "System 2.0.1"—in fact, these are actually System 3.2 Finder 5.3 and System 4.1 Finder 5.5. These confusing numbers also appear in the technical specifications Apple provides for its early hardware and elsewhere in the Knowledge Base.
The source of the confusion is simple. Apple started using version numbers for disks around January 1986, as indicated in parentheses below. You can see them by selecting the disk or mounted disk image in the Finder and using File > Get Info to view the comments. They were also used on the labels of the update disks Apple sent to dealers (an example is shown below). The people who put the develop CD together tried to use these disk version numbers as "System Software" version numbers. Looking at the disk version numbers (in parentheses below), it's easy to see how they came to result in the errors on the CDs and in the Knowledge Base.
System 3.0 Finder 5.1, January 1986:
System 3.1 Finder 5.2, February 1986:
System 3.2 Finder 5.3, June 1986 [disk images]:
System 4.0 Finder 5.4, January 1987:
System 4.1 Finder 5.5, April 1987:
Revised June 1987:
The most unfortunate aspect of this debacle is that a sensible, straightforward approach already existed for the numbering scheme used on the develop CD. It could have, and should have, used the System file version numbers as the basis for its numbering, which make for a nice, neat progression leading up to System Software 5.0 in October 1987.
In reality, Finder version numbers better reflect the evolution of the software itself. Apple didn't release six major Macintosh operating systems in just over four years. Instead, it was more like four: Finder 1.x, Finder 4.1, Finder 5.x, and Finder 6.x. You can even argue there were only three:  everything up to Finder 4.1 (MFS),  Finder 5.x (HFS), and  Finder 6.x (MultiFinder). But this progression became moot the minute the decision was made to introduce the concept of "System Software," which subsumes both the System file and Finder version numbers. Given the initial choice of 5.0 (rather than 6.0, its Finder version number), we may surmise that the idea was to use System file numbers to identify earlier releases, which makes sense. For example, this allows Systems 3.3 and 4.1, which shared Finder 5.4, and Systems 3.4 and 4.1, which shared Finder 5.5, to have discreet numbers.
* Special thanks to Willi Kusche, who gave me access to all of the disk images from the original develop CD.