It's a nontrivial philosophical question whether 'means anything' means anything here.

Oh sure - non-trivial philosophical questions are funny like that.

Anyway, my idea is that for any description of a universe, certain elements of that description will be ad hoc mathematical 'scaffolding' which could easily be changed without meaningfully altering the 'underlying reality'. A basic example of this would be a choice of co-ordinates in Newtonian physics. It doesn't mean anything to say that this body rather than that one is "at rest".

Now, specifying a manner in which the universe is being simulated is like 'choosing co-ordinates' in that, to do a simulation, you need to make a bunch of arbitrary ad hoc choices about how to represent things numerically (you might actually need to be able to say "this body is at rest"). Of course, you also need to specify the laws of physics of the 'outside universe' and how the simulation is being implemented and so on, but perhaps the difference between this and a simple 'choice of co-ordinates' is a difference in degree rather than in kind. (An 'opaque' chunk of physics wrapped in a 'transparent' mathematical skin of varying thickness.)

I'm not saying this account is unproblematic - just that these are some pretty tough metaphysical questions, and I see no grounds for (near-)certainty about their correct resolution.

(Your link is way too long for me to read. But I feel confident in making the a priori guess that Putnam's just wrong, and is trying too hard to fit non-obvious intuitive reasoning into a cosmological framework that is fundamentally mistaken (i.e., non-ensemble).)

He's not talking about ensemble vs 'single universe' models of reality, he's talking about reference - what's it's possible for someone to refer to. He may be wrong - I'm not sure - but even when he's wrong he's usually wrong in an interesting way. (Like this.)

What if I told you I'm a really strong and devoted rationalist who has probably heard of all the possible counterarguments and has explicitly taken into account both outside view and structural uncertainty considerations, and yet still believes 99.5% to be reasonable, if not perhaps a little on the overconfident side?

I'm unmoved - it's trite to point out that even smart people tend to be overconfident in beliefs that they've (in some way) invested in. (And please note that the line you were responding to is specifically about the scenario where there is 'intervention'.)

It's a tricky one - read the paper. I think what he's saying is that there's no way for a person in a simulation (assuming there is no intervention) to refer to the 'outside' world in which the simulation is taking place. Here's a crude analogy: Suppose you were a two-dimensional being living on a flat plane, embedded in an ambient 3D space. Then Putnam would want to say that you cannot possibly refer to "up" and "down". Even if you said "there is a sphere above me" and there was a sphere above you, you would be 'incorrect' (in the same paradoxical way).