Sounds like you are concerned with aliasing of samples, this is where statistics can help, get enough samples and you can remove the aliasing from the results, (I recently was measuring a frequency sources drift, and had the reading dancing between 2 bits of resolution for the entire measurement (was working with what i had on hand), recorded on average 20,000 samples and calculated the min,max,average,standard deviation,etc at a much higher effective resolution, )
As for routing out pins to capture the signal, if they are concerned about the phase delay between 2 pins, then differential routing solves this, as for "the nature of the signal" depends on how much high speed layout practices where paid attention to, as it is very possible to bring out a test point where the signal is properly terminated etc, and remain looking almost exactly the same as the original (capacitive loading will slow the edges a little) with the same jitter and all, just possibly a little rounder eye diagram,