After removing the SDA I2C pull-up resistor I can program the ESP32 with ESP-Prog, so that's good news!
FYI, i did test and try to flash it ,
1. When i connect ESP32-S3 Pin-15 to SDA I2C pull-resistor as you described ? i tested one of my 1-chip Bitaxe_V2 board and it has the same behaviour as before where i could not flash it.
2. When i disconnected the airwire from R19 over to pin 15 on the ESP32 (pink line). i was able to flash the ESP32-S3 without actually pressing the reset button. i know that ESP32-S3 with ESP-PROG it can automatically pull-down when flashing , so you don't have to press the boot and reset buttons manually.
is this a strange behaviour ?
Did you cut the trace connecting SDA to ESP32 Pin-16/GPIO46? I am able to flash my ESP32 with SDA connected to ESP32 Pin-15/GPIO3 (and disconnected from ESP32 Pin-16/GPIO46). Using ESP-Prog I don't have to press the boot or reset button to program.
I suppose using Pin-15/GPIO3 is not the best idea, because like you said it is one of the strapping pins. GPIO3 strapping changes the JTAG source. Not sure yet what effect this has. On the next rev I'll make sure not to use a strapping pin for I2C!