When DST ends you set your clock back 1 hour (or it does it automatically nowadays) in the middle of the night, gaining 1 hour of extra sleep
The joke here is that the guy did the same for Leap Day, setting his clock back 24 hours and gaining 24 hours of sleep, so when his boss called at 2pm he was in the middle of his ~32h night
It didn’t become 2 AM. It was still 2 PM, but on a day that Jenkins already worked.
Jenkins was planning to go to bed on Wednesday the 28th at 10 PM and had his next alarm set for 6 AM on Thursday the 1st. He then adjusted his clock back to Tuesday the 27th at 10 PM.
Why is he in bed saying “it’s the middle of the night” then.
Your explanation does not fit with the comic.
If Jenkins would have said “but i don’t work on Wednesday” and his boss said “it’s Thursday “. That would have fit your scenario.
“It’s the middle of the night!” is an exclamation people often make when they’re woken up. Normally it actually is night; in this case it wasn’t but Jenkins still said that because he had just been woken up and was confused.
But that's not a good joke, IMHO. It strains credulity even in the context of a comic strip and is so counterintuitive and unrelatable that no one here was in the cartoonist's head space.