Random without qualification is used to mean "uniformly". For this specific case (3-SAT), there are only four reasonable readings: both (variables within a clause), and (clauses within the set of all possible clauses) can be chosen with or without replacement. Neither makes a difference in the large n limit.
http://books.google.com/books?id=zyktZTqZSzMC&lpg=PA414&...
is from a reasonable book.
It's true that this phenomenon hasn't been completely rigorously proven, but it's been given "physicist proofs". There's enough evidence that it's unreasonable to not consider it true.
However, where you say this:
.... it's been given "physicist proofs". There's enough
evidence that it's unreasonable to not consider it true.
There had been a lot of evidence around for quite some time that primality was harder than P (assuming P!=NP), and yet it turns out to be in P, even without PvsNP being settled. I'm suspicious. I still believe that hard instances can be found, and that "most" of them will look as you describe, random-ish with the right parameters, but I'm wary about claiming that most things that look like that will, in turn, be "hard."But I suspect we're in agreement, possibly "violent agreement."
ADDED In EDIT: Forgot to say, thanks for the reference.
Easy to generate random hard instances does not at all mean that highly structured "non-random" instances can't be hard. The "phase transition" only means that the fraction that are hard at a given non-critical ratio decreases with n, but there very well could be a large absolute number, that increases with n. The space of problems of size n grows exponentially, after all.
http://www.cs.cornell.edu/selman/papers/pdf/99.nature.phase....