Note: I've entirely rewritten this question! Originally it was just the third formulation, take note of that when reading answers.
Let's say $S$ is a $b$-automatic set, and let's say $M$ is a DFA that defines it when the numbers are read from the little end (right-to-left). Say $\overline{d}(S)$ is the upper density of $S$, and say $\overline{p}(M)$ is the acceptance probability of $M$ on a random infinite string on $\{0,\ldots,b-1\}$ when viewed as a Büchi machine, i.e., we consider $M$ to accept on an infinite string iff it infinitely often passes through an accepting state.
Is $\overline{d}(S)\le \overline{p}(M)$?
Equivalently, we could instead define $\underline{p}(M)$ to be the acceptance probability when viewed as a co-Büchi machine, i.e., we consider it to accept on an infinite string iff it eventually passes only through accepting states, and then ask, is $\underline{d}(S)\ge \underline{p}(M)$?
Also equivalently (I'll skip spelling out the equivalence here), we could restrict consideration to machines $M$ where $\overline{p}(M)=\underline{p}(M)$ -- which really means we can restrict further to machines where from every state it is possible to reach a sink state -- and ask, in this case, do we have $d(S)=p(M)$? (Where $p$ is to $\overline{p}$ and $\underline{p}$ as $d$ is to $\overline{d}$ and $\underline{d}$.)
Also, if the above question is false for natural density, or can't easily be proven for such, could it at least be true for logarithmic density?
Now note that I said that $M$ has to define $S$ when we read numbers from the little end, that's because the question is false if we're reading from the big end (consider e.g. numbers that start with a $1$ in ternary). But it could potentially still be true AFAIK for logarithmic density in that case, so that's another potential question. Although I don't really care so much about the big-endian case...
I have three additional variants on the question I want to ask (because the case I originally care about has more complications I'm afraid), which can also be combined with the variants above. But I'd gladly accept just an answer to the simplified question above, because it's quite interesting on its own.
Complication #1: What if instead $S$ is a $k$-dimensional $b$-automatic set, with the same conditions? So we would be plugging in $k$ random infinite strings on $\{0,...,b-1\}$. Does the inequality hold in this case?
(Is logarithmic density a thing in this setting? I guess you would weight $(n_1,...,n_k)$ by $\prod_i \frac{1}{n_i}$? I don't know if there's a standard version.)
Complication #2: Let's go back to the one-dimensional case. What if now, instead of being $b$-automatic, the set is Zeckendorf-automatic?
In this case, of course, we'll need to adjust our probabilities accordingly. We're plugging in a random infinite string on $\{0,1\}$, but it's no longer uniformly random. Rather, the first digit is a $0$ with probability $\frac{1}{\varphi}$ and a $1$ with probability $\frac{1}{\varphi^2}$, and we use this same distribution after a $0$, but after a $1$ we always put a $0$. (So it's not actually a Markov chain anymore, because it's no longer memoryless... although you could still construe it as one by thinking in terms of $0$ and $10$, so Markov chain techniques could likely still be made to work here.)
Does the inequality hold here? Once again, with natural density if possible or logarithmic density is not.
Complication #3: Combine complications #1 and #2; the set is both multidimensional and Zeckendorf-automatic. You can fill in the details. Unfortunately, at this point we really don't have a finite Markov chain anymore; I don't see any way to construe this case as one.
(This is the case that led to the question -- the set I'm looking at is a two-dimensional Zeckendorf-automatic set. And its machine also obeys the $\overline{p}(M)=\underline{p}(M)$ condition. I was hoping to compute its density, and I would consider this to be the obvious way, but I don't know that it's valid!)
Thanks all!