I work 12hr nights, and I temp whenever I wake up for the day (sometimes 10-11am, sometimes 5pm). I think I probably have more variation in temps than someone who temps at the same time every day, but I can still see a clear temp shift, and always get CH on FF.
I found that if I was trying to temp at 11am every day, no matter when I went to bed, I was getting a lot more variation, because my temps were always higher with 4hrs of sleep vs. 7 or 8. (I'm not sure if that makes sense).
It may take some trial and error to see what works for you.