esptool.py erase_flash command does seem to correctly erase the flash, since it then starts showing:
rst:0x10 (RTCWDT_RTC_RESET),boot:0x13 (SPI_FAST_FLASH_BOOT)
flash read err, 1000
ets_main.c 371
ets Jun 8 2016 00:22:57

But uploading the minimal "Hello World" sketch keeps showing the same ...