Firstly, sorry for my own stupidity. The counterexample is surprisingly simple and elementary.
It is sufficient to take $X = [0,1]$ and compose a countable basis $\beta$ of such intervals that no two have the same endpoint and $X \not \in \beta$ and $\beta$ contains no intervals of the form $(0,x)$ nor $(x,1)$. Then, for any two sets $U,V \in \beta$ with $U \cap V = \emptyset$ we can squeze an (nondegenetare) interval between $U$ and $V$ and for any $U \in \beta$ we have $\# \partial U \leq 2$.
Now, suppose that we manage to select $\beta_0$ such that $\bigcup_{U \in \beta_0} \overline{U} = X$ and sets from $\beta_0$ are pairwise disjoint. Since $\overline{U} \setminus U$ has at most two elements, the set $X \setminus \bigcup_{U \in \beta_0} U \subset \bigcup_{U \in \beta_0} \overline{U} \setminus U$ is at most countable. I will show that $X \setminus \bigcup_{U \in \beta_0} U$ has no isolated points, and it is easy to check that it is closed and nonempty. But a complete space with no isolated points has to have a power of continuum, which leads to contradiction.
Suppose $X \setminus \bigcup_{U \in \beta_0} U$ has an isolated point $x \neq 0,1$. We know that $x \in \partial U$ for some $U \in \beta$. Without loss of generality assume that $x$ is the left endpoint of the interval $U$ so that $U = (x,y)$ for some $y$. Since $x$ is an isolated point of $X \setminus \bigcup_{U \in \beta_0} U$ there has to exist an interval $(z,x)$ which is disjoint from $X \setminus \bigcup_{U \in \beta_0} U$ or, in other words, contained in $\bigcup_{U \in \beta_0} U$. If we select any $t \in (z,x)$ it belongs to some $U = (a,b) \in \beta_0$ with $b \leq x$. But $x$ is already an endpoint of $(x,y) \in \beta$ so, by choice of $\beta$ it can't also be the endpoint of $(a,b)$, thus $b < x$. Note that $b \not \in V$ for $V \in \beta$, since sets in $\beta_0$ are pairwise disjoint, so $X \not \in \bigcup_{U \in \beta_0} U$. At the same time, $b \in (z,x) \subset \bigcup_{U \in \beta_0} U$ which is a contradiction.
The above is a little technical and lacks a few points, but I don't think it's worth to go into more detail here. In fact, one can see that $X \setminus \bigcup_{U \in \beta_0} U$ is homeomorphic to the Cantor set, and thus uncountable.