For plugins that need java runtime

flatpak install flathub org.freedesktop.Sdk.Extension.openjdk17//24.08

For plugins that need tk support

tk only supports x11

flatpak override --socket=x11 --nosocket=fallback-x11 com.sigil_ebook.Sigil

Use pip

flatpak run --command=pip com.sigil_ebook.Sigil install <xxx>