I don't see it that way, but it is up to interpretation of course. It is more of an anti imperialist, anti war story, and having teenagers going through horrors of wars and losing innocence. I can't speak fully for them because I'm not trans, but I know many trans influencers have claimed that a subplot of a character in Animorphs who enjoyed being in animal body moreso than his human body as a trans allegory.

The antiwar message especially rang true considering the series ended during the peak of US War on Terror in 2001. Some fans have argued that Applegate drove the ending into the ditch out of spite because she disagreed with the war (kinda based in hindsight lol). Here's a quote from the author

So, you don’t like the way our little fictional war came out? You don’t like SPOILERS You don’t like that one war simply led to another? Fine. Pretty soon you’ll all be of voting age, and of draft age. So when someone proposes a war, remember that even the most necessary wars, even the rare wars where the lines of good and evil are clear and clean, end with a lot of people dead, a lot of people crippled, and a lot of orphans, widows and grieving parents.