It would be a neat little project to write a tool that renders all those control codes as something more easily read. I wouldn't be surprised if this were in fact the output generated by such a program.
On the one hand I think Iwata could easily have whipped up a little tool, on the other hand I like to think he didn't need it :)
Back in the early/mid 2000s I was involved with the PK Hack community, which was/is a group of people who focus on reverse engineering the EarthBound ROM (documenting and building editors for it, etc). I remember a guy named Flynman was actually putting together a sort of EarthBound scripting language that compiled down into the text engine's control codes. I'm not sure if that ever led anywhere, but it sounded pretty cool at the time. I might dig around to see if I can find it somewhere on the Starmen.net forums
Possibly also something that cross-references all the different GOSUB commands and the FLAG commands to the places they're checked. Then someone could go through and give them friendlier names. Also, you'd want to cross-reference all the text pointers to the text they point to. After that, it shouldn't be too hard to write a tool to do the reverse and pack it back in the original format.
On the one hand I think Iwata could easily have whipped up a little tool, on the other hand I like to think he didn't need it :)