Im a mechanical engineer that works in the HVAC field, so I think I can handle this question.
The carbon filter is basically a resistor in electrical terms. It will provide the same amount of resistance installed at the end of our duct, or right against the fan.
The difference is available pressure. The fan is creating areas of low pressure and high pressure, Low at the inlet of the fan, and High at the outlet. The pressure differential from your space to the fan is greatest at the fan. Therefore, you will move more air through the filter at the location where it has the greatest pressure differential (right at the fan). If the fan has to push air through 6' of ductwork before it even gets to the filter there isn't as much pressure left to push air out of the filter. Basically, the available pressure reduces as the duct gets longer.
Sorry for the long winded technical response.