I was having a discussion about Persona before, and it just reminded how wildly different a lot of us perceive certain characters. I guess that it's only fitting, seeing as this is a series that very much concerns itself with identity and how that permeates itself in the wider world. Still, it made me spend a little more time pondering a character, who, truth be told, has never really endeared herself all that much to me - Naoto.
The statement that her story was just "that she accepts being a woman" irritate me somewhat, because I think that's extremely reductive, and a little dismissive of her actual role within the narrative. It’s not so much that Naoto has to accept that, but being comfortable with how society treats traditional gender roles. Part of my annoyance with the character of Naoto is frankly, not in how she’s portrayed, but how others perceive her. Ostensibly, at odds with how she views herself, and by extension, how society views her, she is at constant cross-roads - either submit or rebel. Unfortunately she feels stifled by the system and negates this in the only way she knows how; invert it by becoming what they accept - a man.
The folly of her character is that she’ extremely logical in an illogical world. Her desired occupations, down to her interests, are all traditionally male-dominated pursuits. Her age, along with her gender all but prevent her from fulfilling her dreams - handicapped by nothing other than inherently flawed social conventions. Her role as the “ace detective” is indicative of this, being an amalgamation of the heroes she came to idolize in media - powerful, assured, males.
It’s almost as if the fanbase forgets this core aspect of the character, and instead what we are left with is comments about how “oh, she’s so sexy.” A lot of people (though not all) always refer to after the fact of her 'transformation', almost as if one (very important) facet of the character doesn't even exist. It completely belays the fact, and people instead are implicit to the grand irony at work.
You can go one further in that it makes a lot of sense how in vanilla most of her skill set was instant kill light or dark abilities, since she probably views the world itself in black/white(even ignoring the literal colors of these abilities, they're also all or nothing). She's so stuck on that, she just figures that the best way to get what she wants is to disguise herself as a man, since she'd have no chance at all as being a woman. I looked at her journey in 4 as her discovering that yes, grey in fact does exist.
Of course, the irony of this as all is as a detective, she's purposely looking away from the truth by being as rigid as she is, unless she honestly thought that she could disguise herself as a man forever, which I doubt. As you said, she had two options, and instead of picking she chose an option that delayed her having to make a choice. Being alone and having a very minimal support structure(family rarely counts in this), it's easy to see why she's become this way, and why she's able to change just by being around the others.