I found one of those secret code things, I think!
This won’t be too spoilery. You can find this portrait of Lionel pretty early in the game:

I thought the plaque at the bottom might say “- LIONEL -” since that one glyph appears in the first and sixth positions. But the game doesn’t have a whole lot of text like this to decipher, except in the newspapers:

And you can see how those paragraphs of text are really just two textures, flipped and rotated. But we’ll come back to this.
I also noticed this sign near a train station:

The shading makes it a little tricky, but you can recognize the I and E from LIONEL, in which case this says “?I??E??.” And, if none of the other letters are L, O, or N, then “TICKETS” is a likely candidate, since this is right by the entrance to a train station. The two Ts are different, but maybe they’re upper- and lower-case variants?
With guesses for L, I, O, N, E, T, C, K, and S, I went back to the two paragraphs that get flipped and rotated to serve as a sort of lorem ipsum in the newspapers. After flipping and rotating and making some more guesses, I found out what the newspapers say:

“THIS NEWSPAPER HAS LOTS OF USEFUL INFORMATION”; “USE THE NEWSPAPER AS HINTS FOR PLAYING THE GAME.” Excellent advice!
The uppercase T above does match the one on the “Tickets” sign, and now we see an uppercase U, which is like the lowercase U but with an extra pixel.
There’s another type of alphabet in this game, seen even more rarely. (Okay this part is kind of a spoiler. Not a huge one. It’s fine.) There’s reason to believe that the big word here is “DUCHESS”:

As far as I can tell, the smaller text is not using the same glyphs as the newspapers. It might be random pixels, but I notice the dates of birth and death begin with the same two “numbers.”
The cool thing is, the very tiny pixel “U” looks like a reduced version of this more detailed “U.” You can kind of say the same thing about the E, H, and S, but it’s not as obvious.
So, here’s how much of the Mina the Hollower cipher alphabet I have figured out based on these texts:

There are a couple more “big” letters in this newspaper ad:

I’m not sure what they’re big versions of, though. This other ad seems to use all “uppercase” letters:

The second word starts with an uppercase T, and the second and fourth letters of the same word look like they could be uppercase Es. Per the headline on the right, it could be “TELEGRAPHY” or something, but I’m not sure. Yeah, that looks like an uppercase A…
There might be more to discover! Let me know if you find anything!