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I'm trying to get an idea of when in the landing process that the pilot decides go/no go.

As a retired ABE (catapults and arresting gear type), I've seen thousands of arrested landings on a aircraft carrier.

The process is a bit different since they're trying to snag a wire, but if the pilot isn't with in the parameters they'd get a wave off.

At what point should/would the tower or pilot have realized that he was in trouble? (Hopefully not too late)

Is there a point where a wave off would/should have been advised?

How's that work in civil aviation ?

Typically, the tower controller will issue a go around if the runway is fouled, (vehicle, aircraft, or other encroachments) but most are done by the pilot, seeing a fouled runway, or flying an unstable approach.

I opine that the skipper of this flight wished to show his prowess by making good a bad approach.

At a very busy airport, it's not likely that they would have even caught it.
At a military airport, they would have picked up the binoculars to verify he had his gear down and then went about their business, and there's less than a 30 percent chance they would have told him to "GO AROUND".
That "GO AROUND" call was probably the supervising pilot telling the trainee pilot to go around.
But the momentum of the heavy aircraft had not enough time to respond, and they're very lucky to be alive.
In an FAA tower, as well as the military towers, their head is on a swivel, so to speak, and there are many things to do, and very little time to do it in.
A glance to make sure there is runway clearance, the landing aircraft ahead of him has exited the runway, or is anticipated to be exited before the one on final crosses landing threshold.
This is a learned judgment call, but is very critical and if the lead aircraft is also a heavy, then there is wake turbulence to be considered, but with both the left and the right runways in use, this is normally taken care of before the radar final controller turns them over to tower.