I'm pretty sure "responsible for 1% of all web-traffic" puts you in the "special experiences" category :)
I guess then, the question is: Why does nobody on the github staff have a similar experiences to me, when they (assumingly) operate at even higher scales?
Or, if they do, why were they not in on the design meetings? Or, if they were, why were they ignored?
However, at least two of these cases are actually something that I test for as part of the practise of systems administration at large high throughput companies.
Transaction ID wrap-around (and auto-increment capacity) are known-knowns in database administration;
The CPU starvation and flap detection mechanisms are also known-knowns in systems administration.
The premise that they came out of the left field is disengenuous at best;
unless I have "special experiences", which is possible I suppose as I was responsible for 1% of all web-traffic at one point in my life... but github should be much higher than that, I am surprised that they haven't tested the first principle assumptions, and controlled for them.
Similar to how a developer sprinkles code with asserts to ensure things that are impossible remain impossible; a sysadmin doesn't take for granted that a service will 'be magic'.