This is something I myself have wondered about for a bit. Toriel has always seemed important somehow despite her small role, why else would the Knight try and kidnap her? The only real logical answer to that with our current knowledge is that she has a bunker code, likely the church one due to her association but as mentioned, why *her?* Why not Alvin, the actual priest?
Well, because it's associated with her in Undertale like you said. Of course, you also mention that this is weird since only we'd know about it. But there's something that connects to all of this which has also bothered me since it has the same problem: it's only makes sense because of Undertale.
The Knight is trying to kidnap people, specifically it's tried to kidnap Toriel, and successfully kidnapped Undyne and Asgore. What do all three of these characters have in common?
They're all major bosses in Undertale.
(Quick side note, I count major boss as all the bosses that show up in the Pacifist ending, that being Toriel, Papyrus, Undyne, Alphys who is filling in for Mettaton, and Asgore. Sans is in this group as well but I'll talk about him later)
I was unsure if this was going to be a true pattern since ones that seemed so concrete in the first two chapters fell apart completely in the later chapters. But it does seem to be consistent so far, so I think there's some merit to it. Of course, there's two characters on that list that haven't been targeted by the Knight yet, three if you count Sans. Let me go over each one real quick and tell you how I think they fit into all of this.
Let's start with the one we have the least to work with on.
Papyrus has been...odd, in Deltarune. Seemingly both important, but not too important (ha). And as each chapter has gone by, he's talked about less and less. Almost like he was just a lure for Undertale fans who wanted to see their favorite character. And I don't mean that in a "Toby Fox tricked all of us!" way, but more in a metanarrative sense. Because of this intentional lack of information, sadly I have nothing to really say about Papyrus in regards to this whole thing. Aside his loose connections with Gaster due to connections with Sans, I don't have much more to say on him.
Unless he's the Knight of course-
Alphys is a weird case. She's not technically the boss of her area, but she did build Mettaton, and it's her you hang out with and learn more about. She's undeniably important to the True Pacifist ending.
This leads to the strangeness of her importance in Deltarune. Or rather, her lacktherof. This wasn't too weird at first, returning Undertale characters seemed largely unimportant or were just references. But as the game has progressed, it's clear this was a deception. Which makes Alphys still being unimportant outside of learning about Undyne and the Mayor's shelter codes really weird. There's two explanations here:
Alphys will get her moment in an upcoming chapter
Certainly a possibility. With the extra traffic in the school due to Noelle and possibly Berdly being added to the group, it could attract enough attention to get Alphys involved. The fact she also replaced Gerson as a teacher and seems to think Susie hates her does seem to be setting up some kind of arc between the two. Perhaps Susie will bring up the free milk, saying how nice it was when her family didn't feed her (as has been implied based on her eating habits and general state of her life). This does likely mean Alphys gets kidnapped, possibly due to finding Undyne's shelter code since we still need that even if we get the guitar. There is another possibility however.
The Knight Already tried to kidnap her
I think this is far less likely so I'll speed through it, but I think it's important to keep in mind as a possibility.
There were two Dark Worlds already open in the school by the time the game started. The Knight is implied to have opened the empty classroom one, but we have no idea who or what opened the closet. Still, this fits the Knight's mo of opening a Dark Fountain near or in the place their target frequents (or has someone else open it), then try to kidnap them.
I have two main problems with this theory. One, then what does this mean for Alphys? Symbolically, with the other possibility I mentioned it lines up with her Undertale counterpart. She helps the crew through someone else while still being largely personally involved. With this possibility, she just...gets skipped? That seems just kinda strange, unless this entire pattern is a coincidence. Which is entirely possible.
My other issue is that it doesn't really line up with what we see in the chapter. King never mentions waiting to kidnap Alphys, he just talks about Lightners as a whole or more specifically Kris and Susie. This whole thing seems more like it's set up as a tutorial, to get the ball rolling on the prophecy, not a kidnap attempt.
That's all I have to say on Alphys, but of course we have one more elephant in the room...
Now, I wasn't sure whether to include Sans as part of this group. After all, he's not a boss. Not on the Pacifist route anyways. But he is there for the ending and is generally a very prevalent character in Undertale. His appearance in the ending can also be explained as him being Papyrus' brother. However, I think it does go deeper in Deltarune if we take the kidnapping pattern into account.
I don't think Sans himself is going to be kidnapped, more so he's connected to the thing all the other bosses are: the bunker. And that's obviously because of his heaps of Gaster connections and the bunker's heaps of Gaster connections. And because it's Gaster, I'm not sure how much of it I can guess. That being said, I think it's possible that Sans is attempting to prevent the kidnappings since in Chapter 4 he's part of the reason Toriel wasn't at the church when the Dark World was opened. That does call into question his motivations since it's heavily speculated the Knight and Gaster are working together, yet someone else likely working with Gaster is directly hindering them. Feels very Sans though.
Sorry for the big long text dump, didn't mean for it to get this big. Your post just reminded me of a theory I've had floating in my mind for a while now since I haven't seen anyone else question why Toriel was being kidnapped and why she'd have a shelter code.
