It's often found alongside natural gas because the rock structures that can trap methane can also trap other gasses, but the original source is different - thermal decomposition of organic matter for natural gas and radioactive decay, mostly of uranium and thorium, for helium.
I agree that the "accumulation over millions of years" is similar (and similarly a potential problem if we burn through all that accumulation).
Helium will leak out of some structures that hold methane. Shale will trap methane and let helium escape. Layers of salt trap both. Thus horizontal drilling and fracking to recover oil and methane from shale produces very little helium.