Okay, here's a longer analysis on what I read now that it's morning (warning: rambling and LONG)
Purple Woman has presence. I spent half of the book wondering what made her stand out to people, but I now think it wasn’t her looks or her circumstances, and she didn’t even stand out in a negative way as I initially assumed. She’s just one of those people who get noticed wherever they go, just by existing. She’s a character.
Yellow Woman is invisible. As @negin very sharply observed, this is purple’s complementary colour. Yellow is one of those people who always get overlooked, always blend with the background. There was nothing special about her being invisible while stalking. She’s just the unassuming kind of person that no one ever thinks about, one of the crowd even when there’s no crowd. This was made hilariously clear when 所長 didn’t even notice her when she was the only other person in his hospital room. Yellow wishes her existence was known like the Purple Woman’s - she wishes she was someone rather than no one, a character rather than an observer.
A small paradox: When Yellow Woman actually got noticed in the past (in that konbini when she was so tired she was unsteady), she never returned out of embarrassment. She’s used to not being noticed, and is not comfortable in a visible role.
We notice Purple’s presence in the course of her work too. Almost immediately all her co-workers and superiors start to fuss over her in an unnatural way. Teaching her how to enunciate, how to take advantage of her position, giving her little snacks, inviting her to drinks, giving her rides so she avoids the bus full of gropers, forming a sexual relationship with her. All this looks like it’s stuff happening TO her rather than stuff she tries to make people do. She attracts attention just by existing.
Meanwhile Yellow has been in the hotel team longer, yet no one notices her, even though they know her. She gets overlooked so much that people start believing she doesn’t like fruit or drink alcohol, even though I’m convinced she never said any of those things. Her rare comments go unheard. Even people physically bumping into her fail to notice her (a slight exaggeration to drive home the point, I think). She’s probably never ever the focus of any office gossip, because she attracts no one’s interest.
Now here’s where it gets a little tricky. All the attention Purple receives changes her. Or maybe, it only changes people’s perception of her. Being the natural center of attention means you’re very visible even when people are looking for someone to blame. The popular new hire can quickly become the cause of all evils in people’s minds, especially as she turned from someone to take care of into someone who needed no one’s help, and was in fact doing well.
Characters tend to be two-dimensional. When people get noticed like Purple Woman, we usually notice only a few things about them, and they necessarily become caricatures of themselves. As Purple Woman changes due to her environment (finding a job, forming a relationship), she becomes unrecognizable in all those who know her only superficially (the shopkeepers first, the children second). Meanwhile, Yellow doesn’t seem to be recognized by either the shopkeepers or the kids, even though she interacts with both of those frequently (by shopping or by giving them goods to sell in the bazaar).
I’m trying to figure out how much agency Purple had in all this. It looks like she only did what she was told (even the drinking the guest’s coffee part and maybe even the becoming 所長’s lover part), like she only ever tried to fit in and do her job well. But then she gets blamed for everything she was taught to do, by exactly those who taught her, in spectacular hypocritical fashion, as is often the case. Well, the helping yourself from the supplies part at least, not the sleeping with the boss part. Although maybe there she also just went with the flow, and maybe thought she couldn’t very well say no. It’s unclear. Visible as she is, we really don’t know what she’s thinking.
Meanwhile, the true thief still goes unnoticed. Even her address is overlooked (only Purple Woman lives near that school, people say). She can steal and she can stalk unchallenged. But she still longs to be Purple Woman, or at least be friends with her.
For most of the book Purple Woman looked like she was in a weak position, and Yellow, as the stalker, in a stronger one. Several times when Purple was wrongly accused, I thought Yellow would step up. The moment she chooses though, is so much more dramatic (and hilarious). She has a plan, and is now ready to act, rather than just watch. She also has a relationship in her mind (she and Purple as one) that only exists in her mind. When Purple finally overcomes her surprise, she does the most natural thing - she takes full advantage of the situation for her own good instead of following the directions of a stranger. We could argue that this is the first time that Purple decides to not do what others expect of her, which sets her free, and lets her gain invisibility (although in real life, running away to a hotel a few stations away after a murder isn’t really a great strategy).
Was Yellow’s decisive (and misguided) action in a time of crisis the turning point for her? She’s now visible, at least in her neighbourhood (not in the hospital room). She fully takes Purple’s place as the main character. And then the book ends, right as she becomes the protagonist she always wanted to be. 
Most hilarious moments for me
When the narrator confidently declares 所長 dead as if it’s something she does every day for a living, then goes on to detail her multi-page escape plan to the dumbfounded purple skirt woman.
When the 所長 jumps when he suddenly notices a whole real person who has been standing in his hospital room for the last half hour or so.
“I’m not 権藤チーフ, I’m Yellow Cardigan Woman!”
And best of all, when the narrator is asked what the purple skirt woman was wearing, and she has NO IDEA. 
