Square Wave from Arduino Due. Is it square enough?

The best way to sample a logic signal is to send the signal down a matched transmission line, such as 70 ohm coax - however to do that you might need something like a 70 ohm resistor in series with 1k, the logic signal drives this voltage divider, the coax samples the small voltage from the 70 ohm resistor (with very little distortion up to 10GHz or more), and at the other end of the signal a 70 ohm input-impedance amplifier can reconstruct the signal. The whole voltage divider setup ought to be in a coaxial cavity with carefully tuned impedance
to ground to match the signal impedance.

Its all very complex and inconvenient and is an acknowledgement that logic signals switch at microwave frequencies to microwave
circuit techniques are required to catch the fastest details.

Standard analog scope probes are a resistive divider and capacitive divider in parallel, which ought to have low distortion in theory, but the
length of coax acts as a complex impedance dependent on frequency at higher frequencies.

When you have a significant area of loop between the probe tip and the ground croc-clip this is going cause distortion
by adding significant stray inductance, and pick up noise by electromagnetic induction as well.