You only use musicals as examples. Is that intentional, because I am sure we could find a lot in plays.
First of all, I think of homely as plain, maybe even slightly 'wrong' looking. Tracy Turnblad is not homely, she is fat. Carlotta is not homely -- I have seen some beautiful, but fat, Carlotta's. In the movie, Minnie Driver was neither, and I thought she was the best thing about the money...she played an over the top diva android a great job.
Re Emmett, I don't know if you are evaluating Christian Borle's looks (homely cute?) or referencing something in the script; but, in the movie, he was played by Luke Wilson, who was pretty handsome -- if in an unusual way -- at the time. Haven't seen him lately, but I doubt he became homely, although he could have put on weight.
I don't think Mama Rose is described as being homely. If so, tell it to Angela Lansbury and Bernadette Peters. (Let's face it, Patti Lupone is homely and, while not homely, Tyne Daly played her as so tight and pinched, she might as well have been homely, ergo not including them).
I never saw any evidence that Mrs. Lovett was homely; maybe a garish dresser and dirty, not homely.
Although I am not sure of the point of this post, I might add:
-- Adrian and Rocky
-- Fanny Brice
-- Lead in i Love My Wife. Lenny Baker WAS homely, but I remember the role as playing up the homeliness.
-- I seem to recall Laura Wingfield described as homely, but that may just be based on the people I have seen play her
-- The Heiress...I can't remember the character's name
-- Alma in Summer and Smoke
-- Josie in Moon for the Misbegotten (or was she just large...I can't remember now)
-- Cyrano in whatever version (homely or ugly?)
-- Can't remember the name of the female lead in The Rainmaker / 110 in the Shade
-- etc.