"The real thing"... it lacks the cultural context here.
She meant it was Honmei choco.
Well, yeah. I thought the implications were pretty clear though: in speculating about Chidori's chocolate, Nanoha recalls all the effort she put into preparing chocolate herself and realizes her own feelings. It'd be fairly unpleasant to read if I left it as "they're... honmei" and put "TL: honmei choco refers to Valentine's Day chocolate that a girl gives as an indication of romantic love rather than out of friendship or obligation" at the bottom.
Some things just don't translate cleanly. This way "the real thing" can refer both to the chocolate and to her feelings. Not a perfect solution, but it gets the point across, sounds more or less natural, and, most importantly, it fits in the bubbles.