Great question. To understand it you need to understand two things, 1) how helium is generated and 2) how helium is trapped.
1) Helium is generated by the decay of radioactive elements, usually uranium and thorium which are both components of granite. The half life of both of these is exceptionally long, of the order of billions of years, so to generate a significant amount of helium from a radioactive granite you need a very long time - hundreds of millions of years.
2) Helium is difficult to trap as it is a light element, so conventional petroleum seals are quite inefficient at trapping it as they still have pore throats. Methane and other hydrocarbons can't escape as they are bigger molecules and can't overcome the capillary pressure of the pore throat except at very high pressures. Helium on the other hand is small and electrically neutral so most of it escapes. To properly trap helium requires an evaporite seal. These seals don't have pore throats as they are chemical sedimentary rocks rather than made of up deposited grains so they are capable of trapping helium (and also much higher pressures of hydrocarbons which is why wells like Dukas that target sub-salt formations often encounter extremely high pressures).
So ideally to form a high-concentation helium pool you need a reservoir that lies on top of a large amount of very old granite basement rock, and then you need an evaporite seal over the top of it. That way you generate a lot of helium and also trap it. That's how you get helium concentrations >1%. There are a number of these in the Amadeus because the basement is granitic, the whole basin is very old so there has been time to generate helium, and there are reservoir rocks (very poor, but reservoir nonetheless) sitting on top of the basement so the helium generated moves into the reservoir rocks. Then in a number of places you have large, thick evaporite units which can act as seals to trap helium.
Now, at Mereenie we are sitting above these salt seals in Ordivician age rocks and a long, long way vertically from the basement rocks which generate the helium. Most of gas in Mereenie is generated from the Horn Valley Siltstone which is an organic shale, not a granite, so doesn't generate much helium (other than a little which would be from uranium and thorium deposited with the shale). Helium would still trickle through the system because helium, as I said, is very difficult to trap so anywhere where there is not an evaporite seal, the helium generated from the basement would eventually migrate through to conventional petroleum traps like the Mereenie reservoirs, get held up there for a bit, then gradually trickle out through the top seal of the Mereenie field and eventually reach the surface, escape into the atmosphere, and then eventually escape the atmosphere and drift off into space.
So that's why for a normal conventional gas field like Mereenie or many of those in the US, a helium content of 0.2 or 0.3% is considered high. But for these deeper reservoirs in the Amadeus that overlie very old granites and underlie evaporite seals, we can get helium contents well above 1% and even up towards 10%. The problem is that the reservoirs are so old and poor (the Heavitree is so tight it is termed a quartzite, not a sandstone) that you won't get much gas flow from them. So 0.2% of a Mereenie well might easily be more helium than 6% of a Heavitree quartzite well.
As to the question of errors in reporting, it is possible as most of these wells were drilled long ago, often in the 60s, and helium is a difficult element to measure. But I don't think they are going to redrill wells and find helium contents that were initially reported as, say, 6%, are actually so erroneous that the true figure is 0.2%. There's a very valid geological explanation for such high helium contents.
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