I have uploaded at least three restaurants to the Gallery, but I play-test everything before I ever upload a lot. I do have a small vase with a single flower in it in the center of the tables in my Old Home Place Bar & Grille. Millie's is a Cafe and hence nothing adorns the center of the tables there. Also, I created Val's Bar & Grille. I don't recall having placed anything on those tables, it's been a while.
Once in a great while food will get dropped on the floor, but that is simply gameplay as in not all servers are up to par. Mostly, the food arrives, and all is well.
I don't know what other lot builders have done. I do have the renovated Chez Llama in my game. Still don't recall having the problems you've cited. Yes, the place has flowers in the center of the tables, but my Sims don't lose their order. It almost sounds like a bug.
I agree with @crocobaura small things in the center of the tables don't or shouldn't upset the placing of plates.
Best of luck @Stormkeep I hope you get it sorted out (please don't mind the little punly). ;)
