When you're running blinky on the HW ESCs, you want to set up the software with the No_Timing software.

The stock software gives you the most amount of timing/boost options, cuz it's assuming you're running a stock motor (10.5+). Thus, you'll be needing more boost/timing outta the ESC, rather than getting more power from the actual motor.

The Mod software gives you fewer tuning options, cuz it's assuming you're running a low turn motor (4.0-6.0ish) and it doesn't want you to overheat the motor or the ESC, hence why some timing/boost options are disabled in the Mod software.

You could also, if you like, use either the mod or the stock software and just set timing and boost to 0. That way, the ESC will still blink as if it were in blinky mode, but if you wanted to add some boost for a super stock class or something, you could also have that option.