So far as I am able to determine, the book Cheaper by the Dozen was never issued under any other title.  I also cannot find any evidence of the authors originally using pen names.  It would have been fairly pointless to use pen names anyway given that the real names of all the family members are used in the book.  One of the book’s authors, Frank B. Gilbreth, Jr., did use the pen name “Ashley Cooper” when writing newspaper columns, but there is no evidence that I have seen to indicate that he used the pen name when he cowrote this book.  My copy of the book says that excerpts from the book were published in Ladies’ Home Journal and that there was a Readers’ Digest edition (both in 1949), but does not say that either had a different title.

As to the origin of the phrase, it was used a great deal by the father of the authors.  This is described in Chapter 3.  It is on p. 16 in my copy of the book.  The authors say that it was “inevitable” that someone would ask their father “How do you feed all those kids, Mister?”  At that point,

Dad would ponder for a minute.  Then, rearing back so those on the outskirts could hear, he’d say as if he had just thought it up:  Well, they come cheaper by the dozen, you know.”

This is the origin of the book’s title.  The phrase was not original to the authors’ father.  It was a well-known phrase simply meaning that things often come cheaper in bulk.  It is not attributed to any individual person.