As mentioned in another thread, I compared lined to unlined by ear and there wasn't much difference. Do you have any measurements to show "lower overall output"?
Nearly all of the vented designs showcased on the site tend to be Larger Low Tuned designs with Chebyshev type alignments. These are "over-damped" enclosures by design typically yielding system 'Q's in the neighborhood of .57 QTC or so with out the requirement of damping enclosure mterial. By completely lining the vented enclosure with absorptive damping material, one is choking off some of the air movement to a degree that the enclosure is designed to take advantage of.
Now, I am not against using well placed damping or reflection absorption materials (8lb ft^3 density mineral wool/rockwool), but lining an entire vented enclosure with it is simply not necessary and begins to be counter productive (increasing impedance peak frequency, further reduction of system 'Q', along with slightly lowering output).
As for specific measurements, output differences will be smallish sometimes more sometimes less. It will be dependent upon the frequency and the system 'Q' in which the driver is aligned with. I have not had a chance to measure this specifically but I will see what I can dig up for you.
