Did the tool provide grid coordinates? I don't recall that. Are there any references to subreddits or other locations actually coordinating these things?
Because the way the US flag appeared certainly looks artificial.
Given the history of trolls defacing such mutable works of art, and their success at doing so (and how people get quite bored/frustrated at fixing it), I find this explanation a bit lacking. I'm sure there were many people interested in helping, but to counter vandalism on such a grand scale, for such a long period of time? Human nature doesn't seem to back that up.
I may very well be wrong: people can and do get together and help with grand pieces of art; but Occam's razor points me towards a smaller number of people running bots.
When r/place was running, things divided into factions as art was placed, and subreddits were even formed dedicated to creating or maintaining a piece of artwork. There were a _lot_ of people, myself included, who really enjoyed being able to do their little part to create something bigger, or maintain it. It was only running for a few days, and was new and interesting for a lot of folks.
Not to say there weren't bots, but keep in mind you could only place one pixel at most every 5 minutes, per user, and that new users weren't allowed to place pixels at all, to discourage people from amassing users just to draw things.
But it's not like only the "creators" could run bots, the "vandals" could as well. so even if you really truly believe it was mostly run by bots, you are still back to square 1 in that you'd need many people working together for a single purpose to get anything other than noise.
But you also need to remember that for the most part the vandals were unorganised. If you got a small group to choose a small spot on the massive canvas, they could get something together in 15 minutes or so, whereas it would take vandals much longer (unless they could somehow organise to completely wipe out one small part).
They created grids and coordinate numbers that told the groups what each and every pixel should be colored.
Then all anyone that wanted to "help" had to do was just look at the grid, and pick a pixel that was wrong to fix.
Like you said, each user had plenty of time in between pixel placements to look at the map and choose their next "fix".