Out of curiosity, I reverted my board back to original firmware and I saw blinking LEDs using sketch posted before.
I have no idea what changed, I haven’t touched the Arduino IDE or firmware in 2 days. I uploaded CiruitPython firmware, then after some time double-tapped the Reset button, fired up Arduino IDE and boom, it works. Too bad I can’t really share any solid advice on what to do in this case, it literally started working on its own.