How can you measure the intrinsic value of oil other than with a market? I agree it should have a non zero value in theory, but my point is that the price of anything is determined only by what someone else is willing to pay for it. The fundamental value could be $1000 a barrel or $0.01 a barrel, the only way to find out is to have a market. Also, just because the fundamental value is > 0, it does not mean that the price must be > 0. If there is no buyer or no functional market, the price can be exactly 0.
I think that's just an extra step in your argument about intrinsic value. Now you have to analyze why the price of energy is $10/hour. That transaction is just another thing determined by a market where there isn't actually intrinsic value that sets the price, but another buyer. You can analyze this series of transactions forever, but you won't ever arrive at a point where the intrinsic value of something is what sets a price directly.
Note: I completely agree with you on the concept of an equilibrium price being a real thing, I just don't think equilibrium is determined by intrinsic value.