I think what you did was update your recovery's font. When in twrp, /system is not your rom's system partition; that's probably mounted elsewhere.Thanks you for your time, but I don't know, maybe I'm not clear enough or I don't really understand what you're all trying to say (more than a possibility lol), this is exactly what I'm doing:
Pastebin version with numbered rows, use it, I'll refer to the exact rows below.
As line #16 shows, I'm actually root, I backup the file and copy the new one in /system/fonts (#18, #21), as lines #26 and #27 point out I have two very different files (different sizes), I change the files permissions (#29, #32) and the output of #35 is actually what I want.
I reboot the device into the ROM, at line #51 you can see I'm not root anymore, and the command at #53 just prints ONE file, the ORIGINAL one (note that the file size is exactly the NotoColorEmoji.ttf.old's one), but I should be able to see both (chmod 644, everyone can read/see those files).
I boot again in recovery, give command at #73 and it says that there are TWO files, the ones I want to have.
Why? It seems like TWRP is working on a virtual file system of its own.
Yes, I have mounted /system as read and write, otherwise it gives an error when you try to access it.
Also, please note that I still see the stock Android emojis, not the ones contained in the new file (the 8MB one), and even if the file is not supported/broken/whatever I should see nothing, not the stock emojis.