There's no conspiracy, I think people just disagree with what "funding" can mean. A bulk sale in the realm of ~20,000 units is equivalent to stakeholder funding when you're at NeXT's scale. It doesn't inherently mean that anything nefarious happened, but there
was a B2B contract written up with the feds, and Jobs accepted it.
The root comment is a perfectly valid question. Since the government wanted to replace the guts with custom Motorola/Intel parts, it's a bit weird that they'd single-out NeXT to sell them an off-the-shelf shell. I'm guessing that Steve's number was in a lot of government Rolodexes after Michael Dell and the others.