You are way over thinking this. First, the flow post filter will be effectively unchanged in terms of laminar/turbulent flow. Second, this is air, not water or more viscous fluid, Adding a couple feet and turns to the intake piping is going to change your pressure drop by like 0.01 psi... Third, the MAF sensor is just that, a sensor, and is capable of accurately measuring a wide range of flow @ varying temp, pressure, humidity, etc. Lastly, the ECU which takes the MAF voltage signal and numerable other variables to determine fueling is capable of operating in both open and closed loop and has short and long trims and will adapt ignition timing, cam advance, and fueling.
I've tuned a bunch of K20Z3's and am anxiously awaiting the capability for 20+ 4runners, but this is not a change that would concern me in the slightest. Pull the battery long enough to wipe the short trims, plug it back in and put it through it's paces.