Well, here's the deal. Assuming, of course, that the replacement Toto fill valve is the Toto TSU99A.X Universal Replacement Fill Valve, also known as the Korky 528GT.
The Korky valve causes the water to shut off basically 1/2" below the point at which the blue top and black body intersect. So...if you line that up with the top of your overflow riser, and click it into place so it's locked, then the water will shut off, as it should, about 1/2" below the top of the overflow, which is generally where Toto wants it to shut off. The one wrinkle is that when you twist the valve head over the stem to lock, it actually rises a smidge. So the water level at shutoff will rise a smidge over where you thought it would be. So, err on the side of the line between black and blue aiming to a point just a smidge below the top of the overflow riser, and then when you twist, voila!, it will be where you want it. If you want the thing to shut off even lower, then just make the head lower on the stem of the valve. Raise the head -- higher water level. Lower the head -- lower water level. It's really that simple. Remember to twist and lock the valve before turning on the water, or the water pressure will shoot the head to the full extension of the stem, and thus be way higher than you want it. Once the water has been turned on, the pressure also serves to push the valve head up against the channel into which you have locked it, further locking it into place. It's very hard to push down with the water on, and it's designed that way, because that way you (or someone who is poking in your tank) can't accidentally-twist it and unlock it.