So far I did order only prototypes from JLCPCB. So I was able to rotate the LEDs manually…
Short story long:
The LED in question is WS2812B-Mini. It for some reason has notch on pin 3. I have the pins 1 and 3 and the notch marked on the silk screen:
I did write email beforehand to ask, how should I rotate the LEDs. Then I did order a simple board with only 16 LEDs to test. No DFM warning and the LEDs were OK.
Then I did order the real prototype and they sent me an email asking about the rotation. We exchanged like 5 emails and I did even send them screenshot from KiCad. However their English is not so good so… And I had to rotate all of them…
Next time I order something with these LEDs everything worked fine…