Generally speaking, your electron package you download, contains asar archive, witch you have to unpack, inject your theme css into a file, and repack it. In this gist I will show you how you can do that. There is also a script to do that all automaticly
Signal package usually resides in /usr/lib/signal-desktop/resources directory. Inside of it there is a file called app.asar witch is an electron archive. Asar app is needed to unpack it, so make sure you installed it. Unpack archive to some directory with command asar e <path-to-app.asar> <path-to-extract-to> for example asar e /usr/lib/signal-desktop/resources/app.asar ..
Now when you have your app unpacked, you have access to stylesheets/manifest.css. You can edit this file with values you want or add an import after the @charset line. If you want to go with the second option you can do it by inserting following line: @import "<your-theme.css>"; and placing your theme in the stylesheets folder. If you are wondering about what values change what, you can get inspierd by this catppuccin theme.
After the injection, you can repack all files and replace your app.asar file. You will need sudo for that. If you are in a directory with your unpacked files you can do that by executting the command sudo asar p . /usr/lib/signal-desktop/resources/app.asar. You should turn off your signal-desktop app for this operation.
If you want all that automated, you can use script provided with this repo. It was based on this, and this.
To run it do chmod +x injector.sh and ./injector.sh <path-to-your-theme-css>.
Remember you have to have asar installed. If for some reason paht to your signal directory is diffrent (in eg. you installed with flatpack), change your SIGNAL_DIR variable in script accordingly.