Let $A$ be a Boolean algebra and let $Ult(A)$ be its Stone space, that is, the set of all ultrafilters on $A$. It is well known that $C=\{\{u\in Ult(A)\!:a\in u\}\!:a\in A\}$ is an algebra of sets isomorphic to $A$ and the elements of $C$ are exactly the clopen sets of the topology on $Ult(A)$ generated by $C$.
Questions: Let $B$ be the $\sigma$-algebra of sets generated by $C$. Does $\{\{u\}\!:u\in Ult(A)\}\subseteq B$ necessarily hold true? If not, is there any standard name for the ultrafilters $u$ satisfying $\{u\}\in B$? Is there any characterization of Boolean algebras $A$ for which $\{\{u\}\!:u\in Ult(A)\}\subseteq B$?
My attempt: A candidate counterexample is the Boolean algebra $A=\mathcal{P}(\omega)$. Then $Ult(A)$ is $\beta\omega$, the Stone-Čech compactification of the integers. It is known that $\beta\omega$ is not first countable, see here (statement 7A). More precisely, if $u\in\beta\omega\setminus\omega$ then $u$ does not have a countable local base, hence $\{u\}$ is not a countable intersection of clopen sets. However, it is not clear to me if this implies $\{u\}\notin B$.
Below we prove that for any Boolean algebra $A$, $\{u\}\in B$ if and only if $u$ has countable character, that is, $u$ is generated by a countable set of generators. As it was shown here or here, no non-principal ultrafilter on $\omega$ is countably generated. Hence, $A=\mathcal{P}(\omega)$ is indeed a counterexample.
Since the character of an ultrafilter $u$ (the minimum size of a set of its generators) is the same as the character of $u$ as a point of the Stone space (the minimum size of its neighbourhood base), the condition $\{\{u\}\!:u\in Ult(A)\}\subseteq B$ is equivalent to the statement that the Stone space $Ult(A)$ is first countable.
Clearly, the Stone space of a countable Boolean algebra is first countable. On the other side, there are uncountable Boolean algebras having first countable Stone space. One example is the algebra of clopen sets of the Weak Parallel Line Topology, which is known to be compact, Hausdorff, zero-dimensional, first countable, but not second countable (Steen, Seebach: Counterexamples in Topology).
Proof. 1 $\Rightarrow$ 2. Since $B$ is the $\sigma$-algebra generated by $C$, we have $B=\bigcup_{\alpha<\omega_1}B_\alpha$, where
Let $\{u\}\in B$ and let $\alpha<\omega_1$ be the least ordinal such that $\{u\}\in B_\alpha$.
2 $\Rightarrow$ 3. If $E\subseteq C$ is countable then there exists a countable set $D\subseteq A$ such that $E=\{\{v\in Ult(A)\!:a\in v\}\!:a\in D\}$. Clearly, $\bigcap E=\{v\in Ult(A)\!:D\subseteq v\}$. If $\{u\}=\bigcap E$ then $u$ must be the only filter containing $D$, that is, $u$ is generated by $D$.
3 $\Rightarrow$ 2 $\Rightarrow$ 1 is clear. $\ $q.e.d.