I did a test import of a .cr2 with the options Copy As DNG, first with no Import Develop preset, then with a Develop preset, and I observe one From Metadata in History:
My guess is that this is an artifact of how Copy As DNG is implemented -- first it converts the raw file to a DNG file and imports it, then it calls Metadata > Read Metadata From File internally to read any develop settings or other metadata that might have been stored in an accompanying .xmp sidecar (if there is one).
Even though you're seeing two From Metadata steps, I think we're pretty safe in concluding that this is a normal side effect of how you're doing the import and you can ignore it.