In order for ostree to pull refs from a mounted filesystem (such as a USB drive) the repo must be in a standard location. Specifically, subdirectories of .ostree/repos.d are checked, then .ostree/repo, ostree/repo, and var/lib/flatpak/repo are checked. By default ostree create-usb uses .ostree/repo, but if you specify another location using --destination-repo a symbolic link will be created for you in .ostree/repos.d.
This command will regenerate the summary file in the destination repo so that it stays accurate, so you shouldn't try to use summary signatures in the destination repo. This shouldn't be a concern because clients that support pulling from USB mounts use signed per-repo and per-commit metadata instead of summary signatures.
ostree --repo=/var/lib/flatpak/repo create-usb /run/media/mwleeds/f6d04c7a-60f6-4ba3-bb96-0f40498675be com.exampleos.Apps app/org.kde.Khangman/x86_64/stable com.exampleos.Apps ostree-metadata com.exampleos.Apps appstream/x86_64
5 metadata, 213 content objects imported; 1 KiB transferred in 1 seconds Copied 3/3 refs successfully from '/var/lib/flatpak/repo' to '.ostree/repo' repository in '/run/media/mwleeds/f6d04c7a-60f6-4ba3-bb96-0f40498675be'.