I think it means, “When all is said and done.” Or, it could mean, “I know what I am talking about and you don’t.” Or, it could mean, “Shut up, the decision is made.” The end of the day is now all day long.
The irony is that, given the technology and workloads that never end, there is no end of the day. At the end of the day, there still is, “It is what it is . . .” which is even worse. The “it is what it is” phrase implies “give up.” It often sounds like, life sucks and work is even worse. Hackneyed phrases get old and meaningless very fast. You are probably using them too much.
At the end of the day, I wish it were the end of the day.