Instead of creating symbolic links, you can set the LD_LIBRARY_PATH environment variable just before executing the runner. The variable's lifetime is that of the terminal it was set in.
For example, on Ubuntu you could reference the Steam libraries and run the game like so:
export LD_LIBRARY_PATH=~/.steam/ubuntu12_32/steam-runtime/lib/i386-linux-gnu/ ./runner
It would be great if the itch desktop app had a way to launch games with user defined options and environment variables. At least, I don't see a way to do it.