While it seems that the Homunculist was designed with a Mauler Familiar in mind, how would you justify your familiar being a Figment? The only thing that I can can think of requires you to take the Cognotogen discovery.
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I would say that the figment was produced due to the consumption of large quantities of psychedelic compounds, Cognatogen optional. The alchemist may or may not realize that the figment is actually a product of his/her mind, and may or may not still consume the substances that caused the figment to manifest in the first place.
For a figment, you don't really need to justify the evolutions granted by the homunculist as being the result of experimentations - the familiar is imaginary anyway, so why not be a little odd?