Does it add mark on positive transition, negative transition or both? Why are you using it to mark? Do you care about the interval between marks? How are you connecting it to the signal being monitored?
Yes, several intervals. Using a crystal, counting it down and tapping the interval of interest. Then create a short pulse off the edge of the sqr wave to generate the harmonics.
Basically a frequency marker is a stable frequency source with a square wave output signal.
They often have well known frequencies like 10 kHz, 25 kHz, 100 kHz etc.
They use a square wave to have as many as possible harmonics of the marker.
A non-symmetrical square-wave will have slightly different harmonic structure which can be calculated as a pulse waveform. See this versus this.
If you are concerned about the difference you can generate an exact 50% duty-cycle by dividing the square-wave frequency by 1/2 using a flip-flop. Of course, you have to increase the input frequency by two to get the desired output frequency with this scheme.