Gotta watch the decimal points! You are talking in thousanths like .004" instead of .040" HUGE DIFF lol.
By taking off material from the head and lessening the cc amount, the secondary comp ratio rises. This increases the engine potential of making more power, (as well as heat), effeciency, and you are basically "exciting" the engine into producing more of what is has. Current engine designs made by the mfg are set and tested to make a certain amount of power on a spec'd octane, stated in the manual. If you increase the CR, your octane will need to go up to keep something called detonation at bay.
Deto can easily described in laymans terms as "pipe bang", or motor knock. What is happening there is the uncontrolled combustion of gases at the wrong "time" as the engine fires off and combusts fuel that is underrated for the motor. It is never good to have signs of deto, the top of the piston gets a sandblasted look, pitting occurs, and the engine can be severly damaged due to low octane with a higher spec engine requirement.
So, if you lower your cyl height by changing the base gasket thickenss, you are retarding the port timing and basically "dropping" all of the ports in relation to the stroke. This tricks the engine tune and will increase the effective stroke and yeild less of a "hit" and add torq to the power curve, with a slight loss of top end over-rev.
Keep in mind, the same rules apply, by lowering the cyl, you just took away volume from the head area so the octane must follow to keep deto away.
The squish clearance is a slightly diff animal in that a tighter squish is typically desirebale bc the bikes usually come through with excessive squish. Performance gains can easily be had with a better running engine simply by tightening the squish AND removing cc's from the bowl so your CR stays the same and the octane can stay whatever is spec'd.
Thats why you see some tuners, (yes, shameless self plug), advertise a "pump" gas head mod in addition to the race head mod. What is usually happening there is the cc's are checked before the head mod, (for ex lets use 15cc), and documented. The gasket surface(s) are cut to reduce the squish clearance,(lets say to 1mm) but no material has been taken away, (so now your cc is 14cc), this means your CR just went up, your octane needs to go up. Conversely, if you take the squish down to 1mm and then REMOVE material from the bowl to get back the 15cc, your octane can stay the same.
The benefit mostly with the head mod and cc reduction is effeciency. This is due to the tighter squish, the engine will run smoother, cooler, you will see a mileage increase as well as increased power. I do this mod for a lot of guys who ride single track and need to stretch out the tank, most see in increase, some more than others, but that depends on conditions, elevation, etc.
If you straight up mod the head for more hit, keep in mind that this will slightly stress out the trans, clutch, engine parts, make more heat, and start to move the line away from reliable to less reliable.
The best answer to most of this is to tailor your needs to your budget and stick with it and enjoy your riding. If you can afford to have a full on race motor that requires race gas, frequent rebuilds, etc then go for it. If you just want a little more and keep the relaibility of the motor as best as you can, it is always a better choice to lower the octane requirements and get what you can out of it in the long run.
Jbub