I think I'm a little obsessive
Yes you are. And read the comment from MarkMLI twice.
What you need is a high end hardware clock.
The hardware of the exactly the same type of PC can differ up and down to 10%.
Otherwise they were not so cheap.
Nor Windows neither Linux were designed to be a realtime system.
Some decades ago when machines were slow the old Unix joke was:
"This OS is designed to fullfill the jobs in finite time"
How will you be shure that while you measure a cron job in the background just started the backup?
Or a windows system just started to enlarge the swap file?
And hundreds more of those situations?
As you said: this is a potential trap, will lead to a ignorant theory.
So buy a high end hardware clock.
What you try is not for these Operating Systems.
And not a software job.
If you don't like a hardware clock then move to a realtime Operating System.
They are not cheap and designed for industrial use.
Winni