Answer by Doruk for Flatpak program can't see all directories

I found an answer from another question:

Your host /usr directory will be mounted under /var/run/host. It mentions that /usr is blacklisted because the sandbox has its own /usr so it may be the reason why it's not available in filesystem options other than host too.

Thus, I can find the directory I was looking for in /var/run/host/usr/lib/lv2 instead of /usr/lib/lv2.