Because it isn't used for much? It's mostly just logs these days. Most data on most systems goes in /usr or /home. I would say the weird thing here is that Flatpak puts runtimes in /var by default instead of ~/.cache or something like that.
User-mode Flatpaks keep things in ~/.local/share/flatpak. This person simply installed a Flatpak in system-mode, which puts it somewhere other users could also run it (i.e. not your home directory).
