It's not a desin defect. It's just that the parts were not designed to work together.

The track cog is designed for a track hub. The freewheel is desgned for a BMX bike. And the flip flop hub is designed for any freewheel/track cog combination so there is no way to be right on target for all combinations.

However, there is a solution. You could use spacers to slightly offcenter the hub so each cog is the same distance from the outer axle nuts. By doing so, you can flip the hub and have either cog on the same chainline. If you want a 'perfect' chainline, you will then need to adjust your chainrings to the chainline you have created in the rear. you can do this with a combination of BB width (preferred), chainring spacers, and crankset selection, depending on how far you need to move the chainring.