The Nasa Space Flight channel on YouTube has been covering all the activity down in Boca Chica like a coat of paint. There is a woman down there name of Mary Pointer, who was about 2 miles away with a professional quality telephoto lens filming at the time of the RUD. I saw exactly what you saw, and was about positive that the flare stack touched off the methane cloud. However, the NSF guys played Mary’s footage back frame by frame. At 30fps, about 2 frames before the Earth Shattering Kaboom! There is a small flame coming from underneath the skirt. You can actually see, in one frame, the shock wave from the vehicle moving past the stack. I’ve not been able to find a screen shot. Check out Nasa Spaceflight.com, or LabPadre. I’m sure they’ll have more and better info than any of the LSM.
Looks like SN4 or support equipment sprung a pretty big leak a short time after the static fire, near the base of the rocket body, which led to the fire/explosion.
This image from the video I mentioned shows both the flame stack and lower part of SN4 engulfed. The explosion/flame front hasn't reached the top of SN4 however.
The image below shows the explosion/flame finally engulfing the top of SN4, but it has left the flare stack. One would think that if it had started underneath the rocket body, the explosion/flame would reach the top of SN4 at about the same time it reached the flare stack and beyond. Not doubting you saw what you saw, but something is odd here and that's what I'm curious to understand. :)
Ref. links:
What Can We Learn From The Explosion Of The Latest SpaceX Prototype?