That's all very interesting, and I totally agree that when you're extracting a resource faster than it's being created, you need to somehow account for the fact that the available quantity is finite.
But I don't see why looking at the energy used to create the resource, or the cost of creating it from scratch, is useful. All that matters today is what's there and how much we use. For example, consider oil versus uranium. In terms of usable energy content, there's a lot more uranium than oil on the planet. I haven't run the numbers, but I'm guessing that stellar nucleosynthesis of heavy elements like uranium is way less efficient than turning CHON into oil with photosynthesis and time. Certainly, if we were creating this stuff today, it would be way cheaper to create a megajoule of oil than a megajoule of U235. But, who cares? We have more uranium, so it ought to be cheaper per megajoule, all else being equal (which it very much isn't, of course).
You say that we're consuming about five million years of fossil fuel production per year, and that there's about 200-300 million years total. The rate is basically ignorable compared to usage, so what really matters is reserves divided by consumption rate. The relevant number is 40-50 years of reserves at current rates. For example, say it turns out that the geologists and petrochemists got it wrong, oil is actually much more energy intensive to produce naturally, and current reserves actually represent 400-600 million years of accumulation. The energetic cost accounting changes dramatically; each barrel of oil now represents twice as much input energy! But our economic situation today doesn't change one bit.
Taking your inheritance analogy, it doesn't matter how much money your rich family line started with, all that matters is how much is there now. It doesn't make a bit of difference to your spending whether your $10 million inheritance is the paltry remains of a $10 billion fortune, or the amazing end result of a $10 investment.
The whole business of input energy and cost to recreate just seems so very arbitrary. For example, why are you counting the cost of the oil, but not the cost of the oxygen you use to burn it? Both parts are necessary, and the fact that oxygen is ubiquitous and easy to access just makes it even more of a subsidy. Shouldn't we be counting not only all the fossil energy needed to create the oil we burn, but all the fossil energy needed to crack all that oxygen out of CO2?