I expect the difference is that when extracting helium from natural gas, the volumes are huge and therefore the purification process is economically feasible.

I expect the difference is that when extracting helium from natural gas, the volumes are huge and therefore the purification process is economically feasible. Trying to do the same for small amounts of helium collected here and there is possible but not economically feasible. It makes more sense to use it as balloon gas.