Gojira54 pretty much covered what I was going to say, but I had the disclaimer because in
this thread (which I believe is the thread for the DL database download you linked to) several people, including Knuckles himself, mentioned having issues with the AI building cities beyond 512. But it sounds like Gojira54 knows more about this than I do.
I have a question; what language is all this written in? How hard is it to look deeply into - for instance, how do editor modders like Quintillus and Steph determine that they can or cannot include certain functions in the editor? Is the exe file in the same language, and does it follow the organization of the Biq in any way?
Well, the original Civ3 editor is written with Microsoft Visual C++ (
screenshot source), so I would assume that Civ3 is also written in C++. The BIQ is
largely documented at Apolyton, so determining whether something can be included in the editor is mostly a matter of figuring out if it's one of the things in that thread at Apolyton. There are a few unknowns in the BIQ format as documented at 'Poly, so occasionally someone comes up with an idea that might possibly be what one of the unknowns are. But these days it's rare to figure out one of the unknowns. Charm is an example of something that took awhile to figure out, and scientific leader toggling for scenarios (at least with 1.22) is something that was somewhat broken for awhile after I joined.
There's also a decent amount of figuring out whether something is likely a hardcoded or an arbitrary restriction. For example, upper limits that are powers of two (such as 512 cities, 8192 units, 32 civs, etc.) are likely hardcoded in - Firaxis probably used some array that of length 9 for cities, 13 for units, 5 for civs, etc. in at least some places, so these would require .exe changes (and as seen, that can be difficult even for wizards such as syn and Knuckles). But some limits in the Firaxis editor appear to be rather arbitrary. For example, it works to set maintenance negative in practice (although I'm not so sure that the AI recognizes this - I haven't tested that enough). It looks like Firaxis probably set zero maintenance as the minimum as a "common sense" limit, rather than for a technical reason.
By and large, I can't actually make head nor tails of the .exe. I studied a bit of assembly language, but it wasn't Intel x86, and even if it had been, it would likely take a long time to figure out the structure. I took a security class as well, which looked at some aspects of deconstructing .exe's, but those were fairly simple cases.
Since Civ3 was likely written in C++, there's also the factor that the .exe code, when converted back into assembly, likely would still be confusing, since the C++ compiler wouldn't always convert it into the type of assembly a human would write. RollerCoaster Tycoon, by contrast, since it was written in assembly, likely has relatively legible assembly. So, even for someone versed in assembly, Civ3 would likely be more challenging and time-consuming than RollerCoaster Tycoon or other games written in assembly language.
The .exe likely does specify the full BIQ in code at some point (after all, it has to load and save BIQs, and it has BIQ/SAV-like structures in memory while it's running), but since it's been compiled, it's easier to figure out the BIQ format by simply changing the .biq (or .sav) in a hex editor than trying to deconstruct the code.