Let $E$ denote a particular (arbitrarily chosen, but fixed) method of representing ordinals as real numbers. Let $\alpha$ denote any large countable ordinal. Suppose that we want to refer to a particular real number $r$ that encodes the corresponding copy of $\alpha$ (assuming that $0 < r < 1$).
For example, consider the following “definition”:
Let $\alpha=\omega_\omega^{\text{CK}}$. The number $r$ is equal to the minimal real number that encodes (according to the algorithm of $E$) any copy of $\alpha$ and is greater than the number $v = \pi - 3$ (that is, there does not exist another real number $w$ that encodes any copy of $\alpha$ by the algorithm of $E$ and satisfies the condition $v < w < r$ ).
Is this “definition” a mathematically correct definition of some particular (unique) real number $r$? If no, then what are possible options to refer to unique real numbers that encode copies of $\alpha$?
One option is using the notion of definability by formulas in a chosen formal language, so that some $i$-th formula will somehow correspond to the definition of $r$ that encodes a particular copy of $\alpha$. But are there any other options?
No, the "definition" you've given is not satisfactory. Regardless of what you mean by "encodes," you would need to justify the existence of a minimal real encoding each ordinal. SSequence's answer explains why this should strike you as implausible rather than plausible.
In fact, there is a precise sense in which what you want cannot be done. That is:
There's just no way around this.
Of course, ZFC proves that there is a way to assign a real to each countable ordinal, that is, that there is an injection from $\omega_1$ to $\mathbb{R}$. The point is that the existence of such an injection doesn't say anything about the existence of such an injection which is in any way nice!
Specifically, at the most abstract level you're asking for a "reasonably definable" injection from $\omega_1$ to $\mathbb{R}$. It turns out that such a thing probably doesn't exist (the "probably" being a response to the inherent weaselliness of the phrase "reasonably definable"). This is a consequence of results in descriptive set theory.
First of all, the mere existence of an injection $\omega_1\rightarrow\mathbb{R}$ at all is not provable from ZF, so to do what you want you'll need to use the axiom of choice in a fundamental way. This tends to rule out the hope of anything so produced being "reasonably definable." And in particular, the axiom of determinacy - which tends to make sets of reals behave incredibly well - proves that no such function exists. "Reasonably definable" objects tend to be compatible with AD, so this provides a further point of evidence.
Now even within ZFC, this cannot be done in a Borel way. Precisely, if $f:\omega_1\rightarrow\mathbb{R}$ is an injection, then we cannot have $ran(f)$ and $\{\langle f(\alpha),f(\beta)\rangle: \alpha<\beta<\omega_1\}$ both be Borel. In fact, if the continuum hypothesis fails, there isn't even a Borel set of cardinality $\omega_1$ since the Borel sets have the perfect set property!
In fact, under additional set-theoretic hypotheses, this can be pushed further - e.g. strong but still fairly reasonable large cardinal hypotheses imply that there is no projective well-ordering of a set of reals of ordertype $\omega_1$, and even no injection from $\omega_1$ to $\mathbb{R}$ which is definable from reals and ordinals.