Actually this is a good point for fine tuning your engine's port timing and you can usually get a few more degrees port duration by lifting the jug (using a shim at a specific thickness or double gaskets). What you can tune for in this area is if you want more low end torque, use a thinner gasket, but if you want a little more on top, use a thicker gasket or use 2 gaskets.
Juice Motorparts sells copper base gaskets in both .025" and .016" and these can be used alone or stacked to fine tune your port duration. I'm using a .025 and a .016" base gasket on mine with a .040" thick aluminum shim to put my ports where I wanted them to be.
You can also deck the bottom of the cylinder on a lathe or a mill if you have access to one or you can have a machine shop mill the bottom to true it up better (I had to cut off nearly .040" to get my cylinder base true so that's why the .040" shim) then stack a few of these copper gaskets to get the hight where you want it to be. It usually takes about .040" (1mm) above stock to see a difference in high rpm power, but you can go higher or lower to suit your needs. Cutting the cylinder base or removing the gasket here is NOT a good place to add more compression since it does effect port timing and duration, but if you need to raise your cylinder up by 1mm or more, you can remove the same amount from the top of the cylinder to keep the geometry the same or to adjust for squish clearance.
When I set mine up with the ports where I wanted them to be my piston was sticking up about 1mm above the deck (I cut .056" off the deck when that jug was on a different engine, but it worked so well I wanted to use it on my second build) so I had to stack a .016" and a .025" head gasket and use a shim on top as well to get the desired squish clearance of .75mm or .030" with the port timings where I wanted them to be with the cylinder raised up .041" above stock.
So, if you want more top end power, raise the jug by .041" by using a .016 and a .025" base gasket, I "glued" the 2 gaskets together with a thin coat of Indian Head Gasket Shellac to ensure a perfect seal, and the copper sealed against the jug and base perfectly too. Raising the jug does the same thing as raising the roof osn the exhaust And transfer ports, but also raises the floor on the intake port so this area would need to be dremeled out the same amount you raise the jug or more to get your intake duration back.
If you want more low rpm power (torque) you can true up the base and lower it down about .040" and keep the piston just below the deck, then adding a .016" copper head gasket up top would give you a really good compression ratio as well as a nice tight squish band. Doing this effectively lowers the roof on the exhaust and transfers and lowers the floor on the intake so the intake will have about 12 degrees more intake duration but the exhaust and transfers will lose about 12 degrees duration so this makes the engine pull harder but it'll lose some top end power and rpm.
Here's the link for the copper gaskets you'd need to do this mod, it does save you a LOT of dremel time when raising the jug since all you need to do really is lower the intake floor or cut out another milimeter from the bottom of the piston skirt to keep the timing there the same as before...
http://juicemotoparts.com/products/copper-base-gasket-for-motorized-bicycle-engine.html Just follow the links to see the rest of them. Also, only the base and head gaskets are solid copper, the rest of his gaskets are rubberized paper coated with copper gasket spray... you can do that at home with a can of copper gasket spray on stock gaskets to save a few bucks.
Hope you got all that... I can explain it all but I'd have to write a fairly thick book to do so...