I think the point is you can't go far with those fuel sources (e.g. you can't have a trucking industry that runs on whale oil).
> Surface level coal my be gone in most places, but large mines full of coal site idle in a lot of places now for economic reasons, and energy poor society may dig out these deposits.
How deep? In a thousand years (let alone a million), will the mining tunnels have collapsed and/or filled with water? Even if the tunnels still exist and are serviceable, an "energy poor society" is probably not going to pump out the many millions of gallons of water needed to get at the coal.
Current humanity has shown very little capacity for heavy investment with only a long range payoff (say taking 100 steps at a time vs. 1 or 2 steps). The problem is with removing all the easily extractable energy resources is that, is it puts the remaining ones too many steps out of reach for someone starting at square one. If you've got 2 6-sided die and someone has to roll 100 with them to get to the next step, it's never going to happen.