The difference is, in the past 10+ years, Neanderthal DNA has been extracted, analyzed & compared to our own.
The major findings were:
- Neanderthals & humans shared circa 99.5% identical DNA moving Neanderthals from a separate species to a sub-species of homo-sapiens, capable of interbreeding.
- Neanderthal alleles in non-African human DNA suggest past interbreeding, around 50,000 years ago, contributing from 1% to 4% of our DNA.
- Your figure of 40% of Neanderthal DNA in modern humans seems to me a bit misleading, since 99.5% of our DNAs were identical to begin with.
So what we're really talking about is that of the one-half-of-one percent different DNA, perhaps up to 40% can still be found, scattered amongst some humans, somewhere.
Bottom line: much of the numbers you arrive at depends on what exactly, and how, you measure, but the overall average of 2% Neanderthal DNA in non-African humans seems to me a fair estimate.
Your 40% refers to the fact that not everybody is the same 2% Neanderthal.
So, some of us, especially (but not only) us males, may be more Neanderthalic than others. ;-)
Some typical Neanderthals, ancient & modern:
Oooooooops!