I should probably also have added that the same site has Kenneth Bainbridge’s final report (a pdf) on the test. It has the particularly thorough listing of those involved in it either as scientists or administrators, though it rather skips past most of the enlisted men present - hence why Maag and Rohrer are a better reference for this particular question. But Bainbridge does give a good account of what they were actually measuring and observing during the test.
I’ve never had the chance to visit the site, but I’m fairly sure that there are no trenches for humans. Between eyewitnesses, documents and photos, I can’t think of any contemporary references to any. (Even the VIPs were face down on tarpaulin sheets about ten miles away from the tower.) The crater and the likes of the base camp were quickly razed and abandoned after the test, so even if there had been any trenches in 1945 they’d be unlikely still to be there as they were originally. The archaeological literature on the site that I’ve seen doesn’t mention any traces of them either.
There were trenches and holes dug for cables and experiments, but these have been documented as such in recent decades.
I don’t think I’ve previously seen references to the document in question and, to date, I’d only skimmed through Walker’s book, but such a report with that date is hardly surprising. The whole question of what future nuclear wars might involve was already being discussed prior to August 1945, at least amongst some of the scientists on the programme. Such speculations then became widespread in all quarters immediately the news about Hiroshima became public.
And even with the doubts about the availability and supply of the weapons, Groves had been careful to ensure that a unit capable of delivering them on Japan was ready long before such doubts were resolved. Provided Trinity was successful, he certainly had a system ready to rain nuclear weapon after nuclear weapon on them as available and required, possibly as part of an invasion plan. (In fact, the evidence is that Groves personally seems to have believed that the Bomb was a war-winning weapon that would settle the matter quickly - as turned out to be the case.)
The issue of the extent to which the top levels of the US government actually envisaged threatening the Soviet Union with nuclear weapons in August 1945 is, to put it mildly, a matter of some historical controversy. Irrespective of that debate, it’s clear that any such plan to comprehensively bomb the Soviets at the time was either hypothetical or fantastic. In practice, the production rate of weapons faltered immediately after the Japanese surrender and the US only had a handful available for a while thereafter.
