Originally the production did not have an intermission at all so I think that's why people play with where the intermission is. By the time I saw it, around its third year, the production had inserted the intermission where it has been traditionally, after Momma Look Sharp.
The rationale behind setting the intermission after He Plays the Violin is that it is exactly halfway through the show.
I did a production where we put the intermission after Cool, Cool Considerate Men then did a reprise of the end of the number to start off the second act.