that's really weird. It looks like the author wrote it with a more powerful system then partly disassembled it. In my opinion this hurts the narrative of this otherwise cool project/article.
If you download the binary and hex dump it, it's a PRG file which contains a 2-byte header ($0801, the load address), followed by a short basic program (816 SYS 2061) followed by the actual code at 2061 ($080d). The actual code starts with LDA $01 but the address is off by 2 bytes (due to the PRG header) so the JSR subroutines are off as well.
For example, the C64 Action Replay cartridge had a built-in monitor. Software machine code monitors and assemblers were also available.