Updating firmware on Adafruit Huzzah ESP8266
I'm confident that I've resolved this now. I'll leave the question here in case it is useful to anyone in the future.

The problem was they way I was downloading the individual bin files from the github repo, using right click -> Save As in Chrome. This downloads a file with the correct name, but it is actually the content of the file's html page, not the binary itself. Downloading the repo as a zip file, extracting the bin files,  and then uploading them to the Huzzah using a single command gave me a properly flashed device.

What happened was I noticed that esptool can upload multiple files in one go so, with the original bin files, I tried the command:


  esptool.py --port COM4 --baud 115200 write_flash -fm dio -fs 32m 0x00000 boot_v1.1.bin 0x01000 user1.bin 0x7C000 esp_init_data_default.bin 0x7E000 blank.bin


and got the following error


  esptool write_flash: error: argument  : Detected overlap at address: 0x1000 for file: user1.bin  


Thats when I noticed that boot_v1.1.bin was way to big to fit in the space between 0x00000 and 0x01000. Examining it in notepad++ revealed that it was html.

A learning experience...