I believe most of ancients Loki were "tests" He Who Remains made on the timeline. As a perfect dictator, HWR could have decided to "play" around the events of Loki's conception and birth several times. Even the main variant Loki being called a "Sacred Timeline criminal" at the beginning of the series was just purely arbitrary. So... seeing a previous female version or alligator version, I find it not really surprising. It was just HWR using and abusing of the TVA pruning rules. In each "reboot", Loki had potentially the possibility to look different. I made a long analysis of season 1 of Loki if anyone is willing to read it.
Am I allowed to post a link from reddit ? I just made a theory about Evolution in the Sacred Timeline. By 2024 in the MCU, the x gene might still be a rare thing. Mutations haven't reach yet what we saw in Marvel comics since the 60es. There is no team in hiding. No secret Xavier's Mansion. When we'll see mutants in the MCU, it would be fresh for us, but also for the world of the mcu. The introduction of mutants will happen naturally along the introduction of new teens discovering their powers. No Wolverine, no Mystique. A blank slate. https://www.reddit.com/r/MCUTheories/comments/orxr9h/loki_time_travel_long_analysis_and_ideas/