The question is as in the title. In the edit history you can find my attempt to formalise the question, but that was a failure, for reasons stated clearly in the comments. Thus, my question is just:
Are omega-consistent extensions of PA always consistent with each other?
$\def\pa{\mathrm{PA}}\def\N{\mathbb N}\DeclareMathOperator\Th{Th}\def\pri{\mathrm{Pr}_1}\def\code#1{\ulcorner#1\urcorner}$The answer is no: in fact, there are sentences $A$ such that $\pa+A$ and $\pa+\neg A$ are both $\omega$-consistent, while together they are visibly inconsistent.
One way to see this is to use the bounded arithmetic complexity of $\omega$-consistency: the set $$\{A: \text{$\pa+A$ is $\omega$-inconsistent}\}$$ is $\Sigma_3$ (“there exists a formula $B(x)$ such that for all $n\in\N$ there exists a PA-proof of $A\to B(n)\land\exists x\,\neg B(x)$”), hence the set $$S=\{A: \text{$\pa+A$ is $\omega$-consistent}\}$$ is $\Pi_3$. Also, if $\N\models A$, then $\pa+A$ is $\omega$-consistent; that is, $S\supseteq\Th(\N)$. However, these two sets cannot be equal, as $\Th(\N)$ is not $\Pi_3$ (in fact, it is not arithmetically definable at all). Thus, $S\supsetneq\Th(\N)$, i.e., there exists a sentence $A$ such that $\pa+A$ is $\omega$-consistent, but $\N\models\neg A$. The latter means that $\pa+\neg A$ is also $\omega$-consistent, QED. The argument actually shows that one can find a $\Sigma_3$-sentence $A$ with this property. (This is best possible: if $A$ is $\Sigma_2$, only one of $\pa+A$ and $\pa+\neg A$ is $\omega$-consistent.)
Another way to prove this is to mimick the proof of Gödel’s incompleteness theorem. Let $\pri(x)$ be the $\Sigma_3$ formula naturally expressing the predicate “the sentence $x$ is provable from $\pa$ using one application of the $\omega$-rule”. By formalizating in $\pa$ the easy arguments that (1) unnested applications of the $\omega$-rule can be collapsed to one, and (2) all true $\Sigma_3$ sentences are provable by one application of the $\omega$-rule, we obtain that $\pri$ satisfies the Hilbert–Bernays–Löb derivability conditions:
$\pa\vdash_1 A\implies\pa\vdash_1\pri(\code A)$,
$\pa\vdash\pri(\code{A\to B})\to(\pri(\code A)\to\pri(\code B))$,
$\pa\vdash\pri(\code A)\to\pri(\code{\pri(\code A)})$,
where $\vdash_1$ denotes provability using one application of $\omega$-rule. Thus, by the standard proof of the second incompleteness theorem, $$\pa\nvdash_1\neg\pri(\code\bot).$$ That is, if $A=\pri(\code\bot)$ is the sentence asserting the $\omega$-inconsistency of $\pa$, then $\neg A$ is not provable from $\pa$ using one application of $\omega$-rule, or in other words, $\pa+A$ is $\omega$-consistent. On the other hand, $\neg A$ is true, hence $\pa+\neg A$ is also $\omega$-consistent.
Another proof (due to G. Kreisel, [1]) :
Using diagonal lemma construct a sentence $K$ such that $$PA\vdash K \leftrightarrow \neg \omega -con(PA+K) ~~~~~~(I)$$ As it was noticed in the Emil's proof, omega-inconsistency is a $\Sigma_3$ property, so $K$ is a $\Sigma_3$ sentence. $K$ is false in the standard model (because if it was true, then by $(I)$ , $PA+K$ should be omega-inconsistent which is impossible, because $\mathbb{N}\vDash PA+K$). So $\mathbb{N}\vDash \neg K$ and (again by $(I)$), $\mathbb{N}\vDash \omega -con(PA+K)$, therefore $PA+K$ is omega-consistent. But $PA+\neg K$ is also omega-consistent because $\mathbb{N}\vDash \neg K$.
Reference
[1] "Necessary and sufficient conditions for undecidabillity of the Gödel sentence and its truth", Peter Clark, David DeVidi, and Michael Hallett (eds), Vintage Enthusiasms: Essays in Honour of John Bell, University of Western Ontario
