One thing that I find helpful for building intuition is considering different perspectives until one of them clicks. So here is an alternative look at the matter in case it helps.
One can rearrange Bezout's Identity as:
$$
y = \frac{d - ax}{b},
$$
and since $y$ is integer, this means $d-ax$ is divisible by $b$; or equivalently, that adding $d$ to $-ax$ (we will work with $ax'$ instead, where $x'=-x$ is a positive number, which can be assumed without loss of generality given the structure of solutions of Bezout's Identity) makes it divisible by $b$, which in modular arithmetic is expressed as
$$
ax' \equiv d \pmod b.
$$
In words: it's possible to multiply $a$ by a number $x'$ such that the remainder of the division by $b$ is $d$ (the greatest common divisor of $a$ and $b$). Similarly you can get: $by \equiv d \pmod a$.
How is this meaningful? You cannot get any remainder you want from any division. Think of $a=5$, $b=10$, any remainder of $ax'/b$ is going to be either $5$ or $0$. In a way $0$ is uninteresting as you can always get that by setting $x'=b$, and Bezout's identity is telling you that you can get a $5$ ($d=5$). More generally, in this rearrangement Bezout's Identity can be understood as a statement about the possible remainders of the division $ax'/b$.
To see why Bezout's Identity is not just providing one remainder, note that from the properties for modular arithmetic we have that: given $ax \equiv d \pmod b$ and an integer $k$, we can get: $kax' \equiv kd \pmod b$. That is: if we know the remainder $d$ from dividing $ax'$ by $b$, then we have that any multiple of $d$ ($dk$) is also a remainder. For instance, consider the case of $a=2$, $b=6$, where the possible remainders of the division $2·x'/6$ are $0$, $2$ and $4$. These are all of the form $kd$ ($d=2$).