To be fair her profile is still going through a revision so I can sense the confusion. I get the confused and intelligent thing confused quite a bit however, so I apologize for that, but yes she is skilled enough to defeat several pirates at once.Even when she's surrounded she can fight several opponents at once.
But if her dash does count as a speed boost, which it likely should and I should change that, she has a very clear cut way of getting away from Jonathan or closing the gap and then establishing a gap once more. It is a speed gap, however, and it'll be incredibly useful to get away from Johnathan when, admittedly, the first attack in to punch likely won't do well. Though she can still fight easily while injured. She can go through entire stages while low on health without needing to heal. She's taken countless beatings from the pirates and can likely take a beating from Johnathan at least for a bit before running away, and then she can stay at a range, which she would do in character to avoid getting hit. She'd understand "Woah, this guy's tough!" And would try to keep the gap between them, and considering how she arguably has a better range game, she could do so. Jonathan would be force to try and close a gap she could easily maintain.
On top of that, I think you misunderstood the chest. She does turn into a chest. She can charge her saucy shot while in the chest, turn back to her normal self, fire, and turn back into a chest immediately after to continue the cycle. She doesn't have any consequence to continuously turning into a chest and she can just spam that. And she can even still smash her hand into the ground, making a miniature shockwave which could knock johnathan off balance or just hurt him in general. It's a spammable move that she'd also do to keep him at range, which she'd do after realizing how much of a threat he is up close. It's not out of character for her to go range, it's just not her first option but after receiving what's likely a bit of a beating by Jonathan it should be assumed that she'd learn to go on the range quickly.
Though I will change her intelligence to further show off her skill, as well as her dash to make it that speed boost like it should be as she moves much quicker when she's dashing around. Thank you for bringing that up, though. I wasn't sure whether or not that would apply at the time, so, legitimately on that, thanks.