There’s a video of an EF5 tornado from the last 24-48 hours that shows continuous lightning in the background.
There hasn’t been an increase in background cosmic rays, so likely the mechanism for lightning generation is likely a continuum in different scenarios. Cosmic rays are one, but not all.
Despite the title, the video shows a really strong mesocyclone as there is a break between the cloud and the ground. The funnel might be visible, but it’s not as big as the video makes you think.
Orrrrrr, there are always tons of cosmic rays of the type that create lightning hitting earth, there just aren't the conditions necessary for those rays to trigger lightning except for when there's a big storm. I imagine the clouds are a different electrical environment than a regular sky and maybe in those conditions a cosmic rays will trigger lightning. Like a gigantic bubble chamber made of our atmosphere.
As others have mentioned you are correct. But Earth's atmosphere has plenty of all forms of matter. A proton can interact with mostly anything and accelerate it. So you can find high energy everything in low earth orbit.