Found some more details about why both MakeFiles and ExtractKickstart is referenced in this context:
The MakeFiles ommand is not only present on the A3000 Install disk, but also on the Workbench 2.1 Install disk. On the Workbench 3.1 Install disk however, there is instead ExtractKickstart:
8.Ram Disk:> version full Install2.1:C/MakeFiles
Could not find version information for 'Install2.1:C/MakeFiles'
8.Ram Disk:> Install2.1:C/MakeFiles ?
Usage: Makefiles dfx: 1.3|2.0 filename
8.Ram Disk:> version full Install3.1:C/ExtractKickstart
extractkickstart 39.3 (1992-08-05)
8.Ram Disk:> Install3.1:C/ExtractKickstart ?
DEVICE/A,TO/A,1.3/S:
MakeFiles usage examples:
8.Ram Disk:> Install2.1:C/MakeFiles df0: 1.3 ram:kick1.3-using-MakeFiles
Insert SuperKickstart Disk in drive DF0: and press RETURN
Reading Header...done.
Reading 1.3 kickstart...done.
Writing 1.3 kickstart...done.
Reading Bonus1.3...done.
Writing Bonus1.3...done.
8.Ram Disk:> Install2.1:C/MakeFiles df0: 2.0 ram:kick2.0-using-MakeFiles
Insert SuperKickstart Disk in drive DF0: and press RETURN
Reading Header...done.
Reading 2.0 kickstart...done.
Writing 2.0 kickstart...done.
Reading 2.0 kickstart...done.
Writing 2.0 kickstart...done.
Reading Bonus2.0...done.
Writing Bonus2.0...done.
ExtractKickstart usage examples:
8.Ram Disk:> Install3.1:C/ExtractKickstart df0: ram:kick1.3-using-ExtractKickstart 1.3
8.Ram Disk:> Install3.1:C/ExtractKickstart df0: ram:kick2.0-using-ExtractKickstart
Not surprisingly, they produce the same kickstart files:
8.Ram Disk:> md5sum ram:kick#?
1978eb9ac6fffb23c428a9502b71cf3b ram:kick2.0-using-ExtractKickstart
565f257f36f7e81ecb5e2aaf03d66953 ram:kick1.3-using-ExtractKickstart
1978eb9ac6fffb23c428a9502b71cf3b ram:kick2.0-using-MakeFiles
565f257f36f7e81ecb5e2aaf03d66953 ram:kick1.3-using-MakeFiles
MakeFiles is actually somewhat more user friendly, as you can start it from the install disk in df0:, then swap in the SuperKickstart disk in df0: when it prompts for it. This is not possible with ExtractKickstart, it requires the SuperKickstart disk to already be in the drive you specify to it on the command line.