The hypothetical reaction you're referencing is an over-simplified version of the actual reaction that is taking place. In strict terms, the hydronium ion does no exist as "$[H^+]$", but rather as "$[H_3O^+]$". The complete reaction (if the solvent is water) would be:
$$\ce{HA(aq) + H_2O(l) <=> H_3O^+(aq) + A^-(aq)}$$
And the equilibrium constant for this reaction would be:
$$K_{eq}=\frac{[H_3O^+][A^-]}{[HA][H_2O]}$$
However, because the solvent (in this case, water) is in excess, its concentration is considered a constant value. This means $[H_2O]$ can be grouped up with $K_{eq}$ (another constant value):
$$[H_2O]*K_{eq}=\frac{[H_3O^+][A^-]}{[HA]}$$
This product is defined as:
$$K_a=[H_2O]*K_{eq}$$
So we have:
$$K_a=\frac{[H_3O^+][A^-]}{[HA]}$$
Even though using $[H_2O]=1$ leads to $K_a = K_{eq}$, that's not the case because $K_a ≠ K_{eq}$
The actual value of $[H_2O]$ at 25°C is:
$$[H_2O]=\frac{\rho_{H_2O}}{M_{H2O}}=\frac{1000 g/L}{18 g/mol}=55.56 mol/L$$
So, if we repeat the reaction using a different solvent "$S$":
$$\ce{HA(aq) + S(l) <=> H_3O^+(aq) + A^-(aq)}$$
$$K_{eq}=\frac{[H_3O^+][A^-]}{[HA][S]}$$
$$[S]*K_{eq}=\frac{[H_3O^+][A^-]}{[HA]}$$
$$K_a=[S]*K_{eq}$$
$$[S]=\frac{\rho_{S}}{M_{S}}$$
In other words, $K_a$ is a function of $[S]$
Since "S" in this case isn't water, it follows that:
$$[S]≠[H_2O]$$
In conclusion:
(1) For the same reaction at the same temperature, $K_a$ calculated with water as a solvent is different than $K_a$ calculated with a different solvent.
(2) $K_a$ depends on the solvent used.