After some more digging I figured it out by adding those lines before starting my app:
DBUS_SYSTEM_BUS_ADDRESS=unix:path=/host/run/dbus/system_bus_socket busctl call org.freedesktop.systemd1 /org/freedesktop/systemd1 org.freedesktop.systemd1.Manager StopUnit ss bluetooth.service replace
sleep 1
hciconfig hci0 up