The following construction works for a pair of qubits and small perturbations with $\|H\|_2\le\frac15$. Remarkably, in this case we can choose operators $A_k$ and $B_k$ independently of $H$.
Basis
Begin by defining pure states
$$
\begin{align}
|\psi_0\rangle &= |0\rangle&
|\psi_2\rangle &= \frac{1}{\sqrt{3}}|0\rangle + \sqrt{\frac23}e^{\frac{2\pi i}{3}}|1\rangle\\
|\psi_1\rangle &= \frac{1}{\sqrt{3}}|0\rangle + \sqrt{\frac23}|1\rangle&
|\psi_3\rangle &= \frac{1}{\sqrt{3}}|0\rangle + \sqrt{\frac23}e^{\frac{4\pi i}{3}}|1\rangle.
\end{align}\tag3
$$
The positive operators $P_i = |\psi_i\rangle\langle\psi_i|$ form a basis$^1$ of the real vector space $L_H(\mathbb{C}^2)$ of Hermitian operators on $\mathbb{C}^2$, so we can write $S=\mathbb{I}_\mathcal{X}\otimes\mathbb{I}_\mathcal{Y}-H$ as a linear combination
$$
S=\sum_{ij}\alpha_{ij}P_i\otimes P_j\tag4
$$
of separable states $P_i\otimes P_j$ with coefficients $\alpha_{ij}\in\mathbb{R}$. We will prove that if $\|H\|_2\le\frac15$ then $\alpha_{ij}\ge 0$.
Dual basis
Operators
$$
\begin{align}
\tilde{P}_0 &= \frac12\begin{pmatrix}
2 & 0 \\
0 & -1
\end{pmatrix}&
\tilde{P}_2 &= \frac{1}{\sqrt8}\begin{pmatrix}
0 & -1-i\sqrt{3} \\
-1+i\sqrt{3} & \sqrt2
\end{pmatrix}\\
\tilde{P}_1 &= \frac12\begin{pmatrix}
0 & \sqrt{2} \\
\sqrt{2} & 1
\end{pmatrix}&
\tilde{P}_3 &= \frac{1}{\sqrt8}\begin{pmatrix}
0 & -1+i\sqrt{3} \\
-1-i\sqrt{3} & \sqrt2
\end{pmatrix}
\end{align}\tag5
$$
form a basis dual$^2$ to $P_i$, so we can compute the coefficients in the expansion of any operator $T\in L_H(\mathbb{C}^2)$ in the basis $P_i$ using
$$
T=\sum_i\langle T,\tilde{P}_i\rangle_{HS} P_i\tag6
$$
where $\langle A,B\rangle_{HS}=\mathrm{tr}(A^\dagger B)$ is the Hilbert-Schmidt inner product.
Coefficients
Finally, $\tilde{P}_i\otimes\tilde{P}_j$ is a basis dual to $P_i\otimes P_j$, so the coefficients in $(4)$ are
$$
\begin{align}
\alpha_{ij}&=\mathrm{tr}[S\tilde{P}_i\otimes\tilde{P}_j]\\
&=\mathrm{tr}[(\mathbb{I}_\mathcal{X}\otimes\mathbb{I}_\mathcal{Y}-H)\tilde{P}_i\otimes\tilde{P}_j]\\
&=\mathrm{tr}(\tilde{P}_i\otimes\tilde{P}_j)-\mathrm{tr}(H\tilde{P}_i\otimes\tilde{P}_j)\\
&=\frac14-\mathrm{tr}(H\tilde{P}_i\otimes\tilde{P}_j)\\
&\ge\frac14-|\mathrm{tr}(H\tilde{P}_i\otimes\tilde{P}_j)|\\
&\ge\frac14-\|H\|_2\|\tilde{P}_i\|_2^2\\
&=\frac{1-5\|H\|_2}{4}
\end{align}\tag7
$$
where we used the facts that $\mathrm{tr}(\tilde{P}_i)=\frac12$ and $\|\tilde{P}_i\|_2=\frac{\sqrt{5}}{2}$ for all $i=1,\dots,4$. Thus, if $\|H\|_2\le\frac15$ then $\alpha_{ij}\ge 0$. We conclude that, up to normalization, $(4)$ is the desired representation of $S$ as a mixture of separable states.
Generalization
The construction above can be generalized to stronger perturbations and higher dimensions. In order to accommodate stronger perturbation one needs to abandon the fixed basis $(3)$ and look for a spanning set of operators $P_i$ that yields small values of $|\mathrm{tr}(H\tilde{P}_i\otimes\tilde{P}_j)|$ in $(7)$. The choice of $P_i$ will generally depend on $H$.
Generalization to higher dimensions is conceptually straightforward, but potentially computationally difficult as the size of a spanning set grows exponentially with Hilbert space dimension. Also, the upper bound on $\|H\|_2$ that admits a fixed basis depends on dimension$^3$.
$^1$ The operators $P_i$ form a simple example of a SIC-POVM. Note that the above construction works for other sets of operators $P_i$ that are not SIC-POVMs. An alternative choice convenient when $H$ is expressed as a Pauli sum is the set of single-qubit stabilizer states
$$
P_0=|0\rangle\langle 0|\quad P_1=|1\rangle\langle 1|\\
P_2=|+\rangle\langle +|\quad P_3=|-\rangle\langle -|\\
P_4=|{+i}\rangle\langle {+i}|\quad P_5=|{-i}\rangle\langle {-i}|.\tag{3'}
$$
$^2$ For a SIC-POVM in Hilbert space of dimension $d$, we have $\tilde{P}_i=((d+1)P_i-I)/d$ (thanks to @Danylo Y for pointing out this simple formula!). More generally, we can compute a dual basis using frame theory. For example, a frame dual to $(3')$ is
$$
\begin{align}
\tilde{P}_0&=\frac13\begin{bmatrix}2&0\\0&-1\end{bmatrix}&\quad\tilde{P}_1=\frac13\begin{bmatrix}-1&0\\0&2\end{bmatrix}\\
\tilde{P}_2&=\frac16\begin{bmatrix}1&3\\3&1\end{bmatrix}&\quad\tilde{P}_3=\frac16\begin{bmatrix}1&-3\\-3&1\end{bmatrix}\\
\tilde{P}_4&=\frac16\begin{bmatrix}1&3i\\-3i&1\end{bmatrix}&\quad\tilde{P}_5=\frac16\begin{bmatrix}1&-3i\\3i&1\end{bmatrix}
\end{align}\tag{5'}
$$
leading to the same bound $\|H\|_2\le\frac15$.
$^3$ In particular, when using a SIC-POVM in Hilbert space of dimension $d$ the coefficients $\alpha_{ij}$ are non-negative if $\|H\|_2\le\frac{1}{d^2+d-1}$. Note that the existence of SIC-POVMs in arbitrary dimensions is currently an open problem.