Do you really need the 20 MOA base? Unless you plan to shoot well beyond 400 yards, even with that short barrel, it might not be necessary for the distances you will shoot.
The VX-3 3-9x40 is really intended for hunting within "point blank range" which to me means a trajectory set up about 2.5 to 3" high at 100 yards, so that you don't deviate from line of sight from end of the barrel out to almost 300 yards. That's where most hunting is done. If you want to shoot beyond that distance, you need a BDC reticle, or preferably matching MOA or MRAD turret/reticle combo.
Depending on base and rifle design, you could put a small shim under the front of the base, between it and the receiver, if the base is very rigid, and bring barrel down some in relation to the scope, if you don't want to buy a new base. It usually works out to about 1 MOA per thousandths of an inch of shim. So a small .010" shim under the front of the base, might bring it down enough to get you sighted in at 100. Do not shim rings in this setting, only under the front of the base and only if the base is very rigid.