I don't think The Variant is actually Loki. I suspect it's really The Enchantress. It may be that The Enchantress is a Loki variant in the MCU, but I think they are throwing us a little misdirect at this point.
Yeah, her appearance at the end made me wonder if that was really her or the "bad" Loki variant in disguise. I don't recall ever seeing her, so I didn't know who she was.