John, yes using port plugs does have an effect on the enclosure tuning besides reducing the port output. The charts you included show the response expected from a vented enclosure in the top curve(i.e., a sharp drop off at 24dB/octave below the 3dB down F3 point). The bottom curve, presumably with the plugs installed, shows the higher F3 frequency, but with a slower 12dB/octave drop off below that which is typical of a sealed enclosure.
This doesn't indicate that an optimally tuned vented enclosure can be converted into an optimally tuned sealed enclosure simply by using port plugs, but situations involving excessive room resonances in the mid-bass frequencies can be partially corrected with the use of the plugs.
