From the Berklee website alumni page:
In 1985, Dream Theater began as Majesty after longtime bandmates Petrucci and Myung arrived at Berklee in search of a drummer who was into progressive rock and metal. They heard Portnoy in a practice room and soon began jamming together. The trio would become the core of one of rock's most virtuosic and heavy bands. After leaving Berklee, the group added a vocalist and keyboard player and changed its name to Dream Theater. Current vocalist LaBrie is the band's third singer and the best fit. His agile voice snarls on the metal tune "The Dark Eternal Night" and then soars sweet and high on the power ballad "The Ministry of Lost Souls" (both from Systematic Chaos). The fleet-fingered Rudess, who joined in 1999 and replaced Berklee alumnus Derek Sherinian '84, is the band's third keyboard player (for more on Sherinian, see "Prepared to Handle Anything," page 13).
I guess you know best, you read a book and this could be wrong, but I was not misleading anyone. I truly always thought this was the actual history and that JP was in fact the mother of DT.
It seems to me that "a book" written and published with the band's approval and participation and which was based almost entirely on interviews with the then current and former band members is a more reliable source than an "alumni page" for a school of which, arguably, none of the band members are actually alumni (because they didn't graduate) and which they only attended for a few months.
Yes, Petrucci and Myung had been "bandmates" before going to Berklee, but whatever band may have existed before they went there effectively broke up as a result of them going there.
And, if JP is the "mother" (or, more accurately, JP and JM collectively), then MP is the "father," so the "my baby" comments were and are perfectly reasonable.