Good point; you're right that his reasoning would be correct if he knew that, e.g., I had used a random number generator to randomly-generate a number between 1 and (total # of beans) and resolved to ask him, only on that numbered bean, to guess the upper bound on the total.

Perhaps to make the bean-game more similar to the original problem, I ought to ask for a guess on the total number after every bean placed, since every bean represents an observer who could be fretting about the Doomsday Argument.

Analogously, it would be misleading to imagine that You the Observer were placed in the human timeline at a single randomly-chosen point by, say, Omega, since every bean (or human) is in fact an observer.

Unfortunately I'm getting muddled and am not clear what consequences this has. Thoughts?

His reasoning would be entirely correct if you had determined the number of beans you draw randomly from between 0 and the total number.

Let's put this a bit more technically: the reasoning would have been correct if the number of beans were a random value drawn from a known (and sufficiently well-behaved) distribution.