I think it's much more likely that it's an accumulation of "seemed like a good idea at the time" hacks, perhaps combined with nobody actually being in charge of

I think it's much more likely that it's an accumulation of "seemed like a good idea at the time" hacks, perhaps combined with nobody actually being in charge of the overall file format. On older computers, you could sometimes save significant save/load time and/or memory overhead by just dumping the in-memory structures/buffers to disk instead of having a nice serialization format/layer. Imagine what a file format looks like if a developer does this every time a new feature needs its own data in the file, for 20 years.