Should the volume of a solute be factored into the volume of a solvent when preparing a substance of a certain molarity?
The only volume that is important in the denominator of your equation is the total volume of solution; neither the volume of solute or solvent are explicitly relevant.

Pragmatically, there is not likely to be much of a volume change when taking a concentrated solution and diluting it.

So with reference to your question, you should add enough solvent to get the proper final volume.  Explicitly, add the 25 mL of stock solution and 'dilute to mark'-- that is add enough solvent so the total solution is 50 mL.  The added solvent might not be exactly 25 mL to make this final volume.