Consistent systems of linear differential and difference equations

We consider systems of linear differential and difference equations \begin{eqnarray*} \partial Y(x) =A(x)Y(x), \sigma Y(x) =B(x)Y(x) \end{eqnarray*} with $\partial = \frac{d}{dx}$, $\sigma$ a shift operator $\sigma(x) = x+a$, $q$-dilation operator $\sigma(x) = qx$ or Mahler operator $\sigma(x) = x^p$ and systems of two linear difference equations \begin{eqnarray*} \sigma_1 Y(x) =A(x)Y(x), \sigma_2 Y(x) =B(x)Y(x) \end{eqnarray*} with $(\sigma_1,\sigma_2)$ a sufficiently independent pair of shift operators, pair of $q$-dilation operators or pair of Mahler operators. Here $A(x)$ and $B(x)$ are $n\times n$ matrices with rational function entries. Assuming a consistency hypothesis, we show that such system can be reduced to a system of a very simple form. Using this we characterize functions satisfying two linear scalar differential or difference equations with respect to these operators. We also indicate how these results have consequences both in the theory of automatic sets, leading to a new proof of Cobham's Theorem, and in the Galois theories of linear difference and differential equations, leading to hypertranscendence results.