You see this as inefficient and maybe you’re right. I think about how little it has cost to run these schools compared to the wealth (financial, cultural, technological) they spin off and to me it looks very efficient.
Don't really buy Levy's thesis of the migration from east to west and Stallman as "the last hacker" hasn't aged well.
But Boston/Cambridge (really Massachusetts generally) did sort of empty out of a lot of tech for a time as minicomputer companies declined and Silicon Valley became the scene. I actually decided not to go that direction because, at the time in the nineties, it would have been a relative cost of living downgrade.
I don't think social relationships and their geography are a particular characteristic of capitalism - let alone US-specific capitalism.
They - and the resulting hub/centralization effects - predate it by millennia. There is no shortage of historical cities or state that became major hubs for certain industries or research. How much of the effort in those places is "wasted" seems hard to quantify in an objective way, but again, the pattern of low-hanging fruit being more available to the first wave and then a lot of smart, hard-working people in the future generations working more around the edges is not capitalism-exclusive.
The Mass scene sort of fizzled in the 90s for various reasons - not dead, but not dominant - and the centre of gravity moved to the West Coast.
So if you were born in CA and studied there - and Atkinson did both - your odds of hitching your wagon to a success story were higher than if you were born in Montana or Dublin.
This is sold as a major efficiency of US capitalism, but in fact it's a major inefficiency because it's a severe physical and cultural constraint on opportunity. It's not that other places lack talented people, it's that the networks are highly localised, the culture is very standardised - far less creative than it used to be, and still pretends to be - and diverse ideas and talent are wasted on an industrial scale.