The most important issue, aside from air temp / density, is the volume of air. Using a 4" to 3" convertor won't change the volume of air, it will just mean that the pressure through that section will be higher. No big deal.
Personally, I'd be more concerned about the volume of air that your air filter can let through as this is a bigger issue. In simple terms, the larger the air filter, the greater the surface area, the easier it can breath and the easier it is for a high volume of air to come through. The other thing about a larger surface area is that the suction force will be lower, allowing the filter to better trap dirt and dust, rather than sucking it through the filtering material.
A good size K&N filter for the FTO is the same one they use on the Calais. It's quite a bit bigger than the small pods that you normally see (probably around twice the length of Boris'). It still fits in, but not with much room

and works beautifully. It will cost a little more, and you will need the adapter, but it breathes better and lets in less dust than the smaller pods.