The stock oval pipe has a csa of pi*(2/2)*(3/2) = 4.71 square inches
New intake is 3 inc round = pi*1.5*1.5 = 7.07 square inches.
New pipe is 1.5 times larger than the original.
therefore readings in new maff tube will be lower than the original figures even if good gains are realised.
your lambda sensors are confirming this within your fuel trims.
In theory at least your new maff reading will equate to 209 * 1.5 =313g/sec which is unlikely, in old money.
But since the original maff sensor does not sit in the center of the tube, its under reading to begin with.
What does this all mean, not much without a dyno, but i would speak to the company about your findings.
Don't forget to post up before and after logs of vagcom 118 to see if the improved air flow can be seen affecting the duty cycle.