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You may be overlooking Hanlon's Razor.
Back in the day there were a number of companies creating personal computers and as many operating systems. Most didn't last long.
The Apple II had a decent mix if graphics and functionality and got lucky enough to capture the education market. Unfortunately, Apple sued into non-existence any company that dared make hardware compatible with their OS.
IBM made the PC and hired MS to write the operating system. Every major corporation on the planet was already their customer so they had an advantage in business. IBM chose not to protect their hardware design so everyone and their brother started to make PC Compatible computers. Competition drove prices down making the platform even more desirable.
As there is much more money in business than in primary education, Software companies generally wrote software for PC Compatible computers first and wrote ports to Apple's OS when they saw a profit in it. Low hardware prices and a larger selection of Software drove much of the market to buy hardware from MS' customers.
So MS wins because it was hired to write an OS for the company that didn't go out of it's way to crush it's competition.
So if there's any collusion w/ NSA types, I'd guess that It's a result of MS' dominance & not the cause.