The VSG’s odd-order harmonics at 100 MHz distort the time domain waveform, making it look like a high-passed square wave, but if you use an external 150-200 MHz low pass filter to remove the harmonics, you can easily clean it up and get a waveform that looks good in the time domain. In the manual we talk about applications that are sensitive to harmonics will require a low pass filter. This is one of those applications.
The TG124A also produces significant harmonics above 16 MHz, but the SA124B removes the harmonics, giving you a good measurement.
A good filter for applications from 100 MHz to 200 MHz requiring low harmonics is http://www.minicircuits.com/pdfs/BLP-200+.pdf
Any application where the output of the VSG goes to a receiver or analyzer will generally not be sensitive to harmonics. In fact, for clocking applications, the harmonics may actually be desirable in many cases to improve slew rate.