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One workaround would be to use an infinite polynomial ring in $x$ and $y$, with $x_i y_j$ standing for $x_{i, j}$.

sage: R.<x, y> = InfinitePolynomialRing(ZZ)
sage: x
x_*
sage: y
y_*
sage: x[3]*y[4]
x_3*y_4
sage: y[6]*x[1]
x_1*y_6