With your small discrepancy or 1-2 inches, no, not really.
I have noticed when I remove half the section in my intake system, the throttle response is better and low-end power seems to come up a bit quicker.
When I put the full intake system on and have my filter down low in the bumper, I noticed better high-end, big revving power gains, but I lost some crisp throttle response and the low-end was more sluggish. Since I daily drive, I took off the second half and have the filter behind the battery in the engine bay.
Now my post contradicts what another member just posted, but your experience may vary.
The engine will breathe the amount of air it needs to as long as it can get it. How that air gets there is the important part, smooth bends as vital.
I also use an E60 MAF, but I did not have to cut anything in my system to have it fit behind the battery. It is a Place Racing 3 inch intake system.