You'll not be flattening the main in a normal situation.

Usually the fractional rigs (say like J/Boats 7/8 situation really would have the check stays much lower than the position of the staysail's head stay.

The use of the checkstay -- besides controlling pumping -- would be to keep the mast in column (i.e., not allowing it to "bow" forward) and just bend the tip of the mast.

If you have a deeper fractional rig, that's a different story.