Assuming Flatpak is correctly installed ensure the runtime and SDK are installed:
flatpak install flathub org.gnome.Platform//3.28 org.gnome.Sdk//3.28
Build using flatpak-builder:
flatpak-builder _build org.midori_browser.Midori.json --force-clean
Test the locally built package:
flatpak-builder --run _build org.midori_browser.Midori.json midori