Calibre metadata search not working when books are transferred via USB

It seems like KOReader is unable to use metadata.calibre located at the root; therefore, the Calibre metadata search doesn't work. Is there a way to fix this?

I see that when I transfer books via Wifi (KOReader > Calibre > Connect), it creates ".metadata.calibre" However, when I transfer books with USB + Calibre, it creates "metadata.calibre"

Both methods used Send to device in Calibre.

Is there a way to get Calibre metadata search from transferring books via Send to device (USB)?