This generator is not fit for generating huge cities. But how massive are cities we are talking about? Have you tried using custom-sized generation instead of warping?
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Unfortunately I don't know any city generators with a similar functionality, please let me know if you find any :)
I'm not familiar enough with ancient cities, so I checked some sources - "Cities of the Classical World" by Colin McEvedy and Wikipedia (Classical Athens). Wikipedia gives larger numbers, it says there were 10000+ houses with ~150K population (15 inhabitants per house is... a lot, I use 6 as a multiplier). That's bigger than a my typical "large" one, but here is a link to a city with pretty close parameters:
http://fantasycities.watabou.ru/?size=70&seed=959965747&hub=0&random=0&elevation...
10K houses, 64K population (as I said I use smaller rate) and the walls are around 1.5 km in diameter. As you can see in the URL, it's a city of size 70. The largest city you can generate via UI is size 200.