Actually, Gnome Software includes support packages in the download size figure. If those were previously installed, the size of the application is 24.6 MB ↓. You can check the actual size of the application by installing from the terminal which breaks down the packages you are downloading. On my system:
ID Branch Op Remote Download
org.citra_emu.citra stable i flathub < 24.6 MB
For me, Gnome Software also shows 24.6 MB because I already have it's required Flatpak runtime installed - it doesn't need to be downloaded again.
This package could also contain some bundled libraries which are not in the runtime which can make it larger than the .deb version.