It is not a design flaw or against any standard.
The Manuals and product-pages more or less clearly state the maximum supported screw length.
The repair of the pictured z10pa d8 was rather simple since only one trace was cut and scratched.
The z10pe d16 WS from my friend was much worse with three screes having scratched and cut many traces.
Though both work as far as i know flawless today.
In his case, he used, i think Alpenfön coolers with clearly stated screw lengths above the supported lengths of the board.
Interestingly, only the screws which were tightened very very strongly, did the damage.
He simply wasn't aware of that problem otherwise it wouldn't have happened, luckily, he knew me : )
I'm not aware that Asus or any other sane OEM would repair such a damage.
With Supermicro i'm certain that they wont touch anything with bigger scratches and or ripped off components.
Jaystwocents did a video on that topic a few years ago, where he drilled through a Asrock X99 board and came to the conclusion that you shouldn't do that if you need it to work.
To repair that, you start with scratching away the soldermask above the damaged traces until you see the copper trace, then you pit tin on it.
Depending on the damage, that's enough when the cut wasn't wide, and the solder bridges it, or you need to put a "wire" on top of the trace to bridge the gap.
That's basically it.
There are a few tricks but in general it's simple.