So, Image #2 shows you right off the bat we are not examining the complete Y chromosome. This is due to the complex nature of the Y chromosome in the missing/unknown region and the limitations of past and current testing technology to sequence the missing/unknown region. And yes, that missing/unknown region is around HALF of the Y chromosome.
Images #3 and #4 illustrate that NGS testing like BigY tests target a smaller region of the Y chromosome than can be examined. They deliberately exclude that extra segment, which is around 5M locations long. Also, it illustrates that NO two tests are identical. EVERY test will have some missing locations it just does not examine. The missing locations are not consistent from test to test, but are random. This is not just between two different men, but occurs even if the same man took the test 2 different times. His 2 tests will NOT be identical, except for pure luck, which is highly unlikely.
Since we have no data from the missing locations, we have absolutely no idea what is happening there; so we cannot compare any 2 men precisely. In some instances, if the missing locations include mutations that are upstream of where the man's terminal clade appears to be, then THOSE mutations are ASSUMED to be present.
Images #5 and #6 illustrate that while 30X WGS tests examine that extra segment, they also have missing locations; although typically fewer and smaller than the NGS tests like the BigY. Again, those missing locations are random and inconsistent in occurrence and prevent us from comparing 2 men precisely, and assumptions of the existence of upstream mutations are still made.
This is why sometimes it is necessary to do an individual Sanger test for a mutation that one man clearly has, but it is unknown for a second man because the mutation is in one of his missing locations. It is a frustrating situation, but it is what we are stuck with given past and current testing technology.
Image #7 illustrates what the near future will hopefully bring: sequencing of the Y chromosome from end-to-end with NO gaps/missing locations, at an affordable price. This is what they finally accomplished and announced in February of this year, although the price was far from affordable, being more than US$50K just for lab costs alone, not counting man-hours invested. But again, hopefully the testing process can be streamlined and made affordable, that is, less than US$1000.
