When Cantor published his seminal diagonal argument, he used binary code and did not distinguish the real numbers 0.1000… and 0.0111…
This is not relevant for the proof.
See :
and
For detailed discussion of Cantor's proofs:
1873 proof: Dauben page 50 and Ferreiros page 179.
1877 proof: Ferreiros page 190-2. See page 190, for the presumibely source of the misconception.
1891 proof (the diagonalization one): Dauben page 165 and Ferreiros page 287.
For an early textbook version of the diagonal proof, see:
"we now define a number [...] $b=0.b_1b_2b_3 \ldots$, where $b_r$ is never the same as $a_{rr}$."
Regarding the purported "mistake" in the diagonal proof, see e.g. Robert Gray Georg Cantor and Transcendental Numbers, The American Mathematical Monthly, vol. 101, 1994, page 823.
The "general" theorem consider an enumeration of an infinite sequnce of infinite strings of symbols, with only two symbols : $m$ or $w$.
The proof does not rely on any property of real numbers (or their representation).
It is easily "applied" to the real numbers through their binary representation.
In the case of number with a "dual" representation, both representation must be included into the enumeration.
We can consider a simplified case :
$$a_1=0.000 \ldots$$
$$a_2=0.011 \ldots$$
$$a_3=0.100 \ldots$$
$$\ldots$$
and apply Young's procedure; we will get :
$$b=0.101 \ldots$$
because: $b_1 \ne a_{11}=0$, $b_2 \ne a_{22}=1$, $b_3 \ne a_{33}=0$.
The presence of $a_2$ and $a_3$, that are two "dual" representation of the same number, does not invalidate the diagonalization.
With this simple example we see that also if two members of the list, say $a_n$ and $a_m$, are two distinct representations of the same number we have that :
$b \ne a_n$, because $b_n \ne a_{nn}$
and :
$b \ne a_m$, because $b_m \ne a_{mm}$
and this "works" irrespectively of the fact that $a_n=a_m$ or not.