A best attempt at answering my own question, provided for archival purposes.
Preliminary research insights:
Regarding ERT12, without fully understanding how to translate the findings:
A. If the problem is massaged into one without sub-grid constraints, it can be represented by $(|X| \times 2 \cdot |X| + |X|^2)$ constraints in +$1$-in-$k$-SAT form, which is $(3 k^2)$ constraints, where $k = |X|$.
B. Adding $i$-many $\ell_{i,x}$ clues / labels reduces the constraints to $c = (3 k^2 - 3 i)$.
C. Any +$1$-in-$k$-SAT form problem can be written as a "$k$-SAT problem and $\frac{1}{2}k(k-1)$ of $2$-SAT problems." So, that would be $c$-many $k$-SAT problems and $\frac{1}{2}ck(k - 1)$-many of the $2$-SAT problems.
D. Assuming $r$-many runs of an $\mathcal{O}{(y)}$ algorithm can be denoted as $r \cdot \mathcal{O}{\left( y \right)}$, then $r \cdot \mathcal{O}{\left( g(n) \right)}$ $\in $ $\mathcal{O}(r \cdot g(n))$;
E. And, Assuming $n = c$ (unjustified??...)
F. If $\mathcal{O}{\left( k\mathrm{-SAT} \right)}$ $\in $ $\mathcal{O}(f(n))$, then $c \cdot \mathcal{O}{\left( k\mathrm{-SAT} \right)}$ $\in $ $\mathcal{O}(c \cdot f(c))$
G. If $\mathcal{O}{\left( 2\mathrm{-SAT} \right)}$ $\in $ $\mathcal{O}(n^2)$, then $\frac{1}{2} ck(k-1) \cdot \mathcal{O}{\left( 2\mathrm{-SAT} \right)} \in \mathcal{O}{\left(k^2 c \cdot c^2 \right)}$
H. So, if $s(L_i)$ is an algorithm $s$ which solves $L$ given $i$ labels, then
$$\mathcal{O}{\left( s(L_i) \right)} \in \mathcal{O}{\left( (k^2 - i) f(k^2 - i) + k^2(k^2 - i)^3 \right)}$$
And, IP01 offers:
A. If $f(n)$ is an exponential function of the form $2^{\delta n}$, where $\delta > 0$, then as $k \to \infty$, $\delta$ is proven to be "strictly increasing infinitely often" ($-§$Intro):
B. Then, the polynomial terms are negligible, giving
$$\mathcal{O}{\left(s(L_i)\right)} \in \mathcal{O}{\left((k^2 - i) \space 2^{\delta \left( k^2 - i \right)} \right)}$$
Best-case scenario for solver:
\begin{bmatrix}
? & \ell_{0,1} & \ell_{0,2} & \ell_{0,3} \\
\ell_{1,0} & ? & \ell_{1,2} & \ell_{1,3} \\
\ell_{2,0} & \ell_{2,1} & ? & \ell_{2,3} \\
\ell_{3,0} & \ell_{3,1} & \ell_{3,2} & ? \\
\end{bmatrix}
Worst-case scenario for solver:
\begin{bmatrix}
\ell_{0,0} & \ell_{0,1} & \ell_{0,2} & \ell_{0,3} \\
\ell_{1,0} & ? & ? & \ell_{1,3} \\
\ell_{2,0} & ? & ? & \ell_{2,3} \\
\ell_{3,0} & \ell_{3,1} & \ell_{3,2} & \ell_{3,3} \\
\end{bmatrix}
In the best-case, there's no ambiguity to the puzzle. Each row and column is missing at most one label. Surprisingly, the complexity for solving is still $\mathcal{O}(m \cdot k)$. This is seen from the solving algorithm: "for each row, $m$, missing a label, create a copy of set $X \to C$, then remove each existing label in the row from the set $C$, the remaining label fills in the blank space."
In the worst-case for a solver, the clues leave a sub-square in the center of the larger Latin-square, whose rows & columns are missing the same labels. It can be seen that the sub-square is itself a Latin-square whose sides are of length $\sqrt{\left(k^2 - i\right)}$ with no provided clues. So, in the worst-case, the solution to the puzzle is perfectly concealed.