No, the block is designed with the crankshaft offset .265 from the center of the block . . . it is a deliberate part of how the engine is supposed to work. The rod lengths, valve lengths and all components are the SAME from side to side (as they should be).
Do not attempt to alter the decks or valve seat depths to make the valves the same height to the decks - that will ruin the block. There is nothing wrong with the design - it is just important that you know about it and don't attempt to "correct it".
If you're bored, you can look at the drawing that I did for a 4 1/8" stroke crank in the block (based off of Ford's original blue-prints). It is a bit hard to read - lots of details.
Note: This is for the 59A through 8BA blocks - the valve angles were different from 32 - 42.
FlatheadFordEngineCrossSection-59A-8BA.PDF