This isn't like Halo because we're not talking about gameplay, we're talking about story contrivences. All you need to do is justify this shit. It aint that hard.
First, identify the problems.
First up, am I expected to believe that she had one shirt, total? And that her only 'shirt' was actually a bikini top that barely covers her nipples?
Second: Given that she already dresses like an nudist, why is her losing her bikini top a big deal?
Third: Why is she willing to continue risking her clothes for no reason even after having her 'shirt' stolen? (bathing seemed like a totally random choice, and the outcome was entirely predictable)
Ok so the solution is to start her off with actual clothes. The shorts are fine but the jacket covers nothing and the 'shirt' aint working.
Start her off with a a real t-shirt (probably white) then use story events to sabotage them somehow.
If her shirt is white then you can play with water and have it turn see-through for a scene or two, then maybe a monster tears it or a slime dissolves it.
Justify her having no spares (poor? possibly a fire in her home destroyed all of her clothes?)
She could have a full-sized jacket that gets torn or burned or something and what's left is converted into the half-jacket that she starts with.
If that jacket and her bra is all she has left, then it'd explain why she wears it all the time.
As for her bathing, maybe she had to wash the slime-acid off before it burned her skin. Justify shit.
Not sure how you could justify the beach-scene though. The entire point is that she doesn't want to run around half-naked, so convincing her to willingly run around totally naked while interacting with people seems like a no-go.
There's also the fact that her 'friend' puts forth no effort to convince her to do it at all, but she agrees anyway.
You need to cook up an excuse for her to not have any clothes, and to have a bucket of paint nearby. Make it so that her choices are between the paint bikini or being openly naked.
Maybe she's taken a part-time job handing out fliers to try to earn money for new clothes, and her boss supplied a swimsuit for her to wear on the beach.
Something goes wrong, the swimsuit falls apart at the far end of the beach. She has to get back to her bag of clothes without being seen, and her friend suggests the paint as a stopgap.
Then you just need to have her boss be blocking the way to her bag and not be willing to move until she hands out all of her flyers (preferably because the boss doesn't recognise why she so desperately needs to get changed, because he's fooled by the paint)
There. It's not perfect but I put atleast a little bit of effort into justifying her choices and actions.