Then you have to remember that Bubblegum Crisis was based off of Blade Runner*: Sylia might have been a stand-in for Rick Deckard, who is rumored to have been a replicant himself. Both of them made careers out of putting boomers/replicants out of commission and have distinct memories of childhoods that could have been implanted.
The remake's creators kind of ran with the idea that Sylia was the product of boomer experimentation by her father, which resulted in her being mentally unstable and in the creation of her boomer twin, Galatea. Also, Mackie - kind of a useless character, really, in the original - turned out to be an advanced type of boomer, as well, so it gets me thinking that the concept was already well-discussed in notes about the original. Or perhaps they were just inspired by the fan theory that had been posited shortly after the series began. Who knows??