Two characters dont have to take the same attack or be in the same circumstance for their endurance to be measured. Why do people rate Akainu's endurance highly? When ni other top tier took the same attack in the same situation
Because that's not the problem here, if you simply said Zoro has the best endurance feat on the rooftop, no issues. But instead you
are the one who decided to compare the two situations as proof
for Zoro's superior endurance, when the comparison doesn't even begin to make sense.
Already gave you the bullet proof vest example, to show the fault in your reasoning, I'll even give you another example regarding this notion of overall damage taken:
-Person A gets stabbed, continues to fight through it.
-Person B gets punched on the chin without being able to defend and gets immediately KOd.
Being able to pull off one (fighting through a stab) doesn't excuse you from falling to the other (getting KOd to a punch), despite in many cases the stab being the more "damaging" of the two. Heck person A and B can be the same damn person. Getting knocked out is more than just the net damage taken.
By default fighting through the wound is the better endurance feat because person B didn't even endure anything, they got KOd. But getting KOd is not proof you couldn't do the other, or vice versa.