hey hey hey, and 05's. Don't be shorting us 05's with the S-VT (it is actually Sequential-Valve Timing, not VV-T on the Mazdas).
Generally you are right that short stroke engines have long rods and long stroke engines have short rods, but that is not always the case. Some engine from the factory have short blocks as opposed to tall blocks (in regards to the height, not the length is is normally the case when you are refering to short or long blocks). Some engines are designed so that even with a very short stroke (generally having a shorter stroke then bore is considered a short stroke motor) they also have very short rods. Others have very long rods with long strokes as well...of course these blocks also tend to be very tall.
A long stroke and short rod is going to be very benificial to producing torque low down, but it is going to suck for high engine speeds. The MZR motor seems to be built such that it produces very good high rpm power. The lengthening of the stroke (and shortening of the rods) in the 2.3 adds the benifit of a fair bit more torque low down...but it does not pan out in the upper rpms that way. It produces some extra power, but only a little bit.
The 2.3 produces 156hp in the revised SAE system, the 2.0 motor produces 148hp in the revised SAE system. That means that by lengthening the stroke they gained 5.4% more power. The motors produce the same torque as before, or 150lb-ft and 135lb-ft so the gain in torque was 11.1% more torque. You can see just how benificial to torque it is by adding a longer stroke and the fact that it is not that benificial to upper RPM engine breathing and production of power. Something else to keep in mind going from 2.0 to 2.3L (actually it is about 2.25L, they round up) is an increase of 12.5-13%...you can find the difference in torque by taking into account that they added balance shafts that eat up 2-3lb-ft of torque...which is enough to about bump the increase in torque up to 13% if the balance shafts were not there.
Anyway, back to boring. I think you could get the motor to 2.1L by boring the stock liners, but I doubt you could get it higher then that...at least not much. If you are going NA then I highly suggest you do this. If you are getting custom forged pistons anyway it is no cost increase there and you are going to need to get the cylinders honed anyway for the new pistons and rings, it is a small cost increament to get the cylinders bored out at the same time as being honed. Maybe an extra 100-200 all around to increase the bore if you are adding new higher compression pistons.
-Matt