So I've been thinking about how it's being heavily implied that the Neighborhood puppets are supernaturally linked to their voice actors. When Poppy panicked in her bricked-up house and simultaneously saw an open and closed door, it was similar to ink-and-color Eddie staring at his puppet hand and struggling to move it. The terror of realizing there's another world out there, another you out there, perhaps, had to be terrifying for both of them.
And yet, these links are paramount to their existence. Without them, they'd be voiceless, unable to express themselves, unable to interact with others. It's like- imagine your favorite cartoon character's voice actor being replaced. It's still that character, technically, but it isn't them in the same way it used to be. Every voice actor will bring something different to a character, for better or for worse. It's a very precarious balance between innovation and familiarity.
It's notable that Frank and Sally were present during both Eddie and Poppy's breakdowns, and that both of them have had brief moments of what might be lucidity on the WHRP pages- Frank with the bug messages (though these might be Wally's doing), and Sally with her scary story on the Halloween record. Sally is vain as all get-out and seems to have a bit of a mean streak with Eddie, but she clearly knows more than she lets on. Frank isn't just grumpy, he has a wide range of emotions: singing about his orderliness and winter woes, laughing with Julie, being generally helpful.
Wally is the only puppet who is said to be unclear as to whether he HAD a puppeteer or not. His backstory is by far the most mysterious, other than Home's (and that clock/watchtower/lighthouse thingy, whatever they are). When he interacts with the in-universe You on the website, he sounds noticeably drained and frustrated at being unable to establish the kind of connection he wants to. When the Neighborhood findings are allowed to be observed without interference, he sounds more confused and melancholy.
What I'm trying to get at is- if all the Neighborhood folks had a human they were linked to, if that human died or left, they became functionally lifeless. Wally, Frank, and Sally are exhibiting traits of sentience beyond their assigned roles. I think this means that either Frank and Sally's humans are still alive, still tethered to them, or they found new humans to inhabit among the WHRP.
Think about it. All Wally has wanted through this whole story is for somebody to "let him in". He's tried with the Question-Answerer, he's tried with the in-universe You, he's trying with W, but nothing works. The human-puppet links that came so instictually to his friends are quite difficult for him for some reason, so he manipulates what he can- the website, audios, images- in order to be seen.
Do I think Wally's being manipulated by some outside force, like Home or that clock-thingy? Yes. Why is he still sentient when he's missing the human link he needs to be? There's clearly an exception to him, but I'm not sure what. Maybe he can just get by with the smaller, temporary connections he forges when communicating with W.
Wally's actions are absolutely not entirely his own. There's more pieces to the puzzle we're missing.