When it comes to the matching networks, I create a plot for the unmatched antenna, then open the matching screen, which looks like:
When choosing for comparison purposes I tend to stick with L networks, and choose whichever one for a given antenna produces the least amount of loss. If I used a Pi or a T network I could artificially manipulate the Q reading and to an extent manipulate the output, which is not what I want to happen. I could also use the stub match, although I generally don't tend to.
Comparing plots for matched and unmatched antennas, I'll start with an end fed half wavelength antenna.
As you can see, the plots are the same, except one is attenuated slightly. Here is the data for the plots shown above.
With these screens you can see the effects of the matching network compared to no matching network. The impedance is much lower, as is the SWR reading. Other changes, such as the efficiency readings are adjusted as well.
Comparing various antennas in a given environment, some antennas will be affected more by matching than others, for example, an end fed half wavelength antenna vs a center fed half wavelength antenna. The end fed half wavelength antenna will have far more matching losses than the center fed half wavelength antenna, which likely has none as matching should not be needed. In the end it is just one additional factor to consider to get more accurate results...
A note on using this matching feature, it assumes a low loss L network. This can be a problem as many antennas (the a99 for example) don't have a matching network that even resembles such a low loss matching system, so matching for said antennas will always be a bit optimistic. I have yet to find a sure way around this...
The DB
EDIT: Odd, in one of my browsers the pictures don't show but can be right clicked and downloaded, and in another browser they show fine...