Interesting. I think it’s undeniable that winning the war has changed their fates. The similarities between both books are only on Jake and Rachel’s parts, but the rest is all different, for the better. But I suppose, the conclusion in 54 IS the ‘less worse’ outcome in comparison to #41: The Familiar, and even to the Ellimist’s ‘most probable future’ he showed the Anis in #7: The Stranger.
The issue I have with #41 is that it’s hard to say if the unidentified ‘aliens’ that spoke at the end there were working along the same lines as the Ellimist (showing a fact), or if they just selected Jake when he was down for the sake of testing the arbitrary choices in a sentient being such as a human (experimentational). Yeah, it's obvious the Animorphs lost the fight in that scenario, it was believable, but there were a few inconsistencies which were quickly and covered up.
I don’t think that the scenario in #41 is real in terms of the characters, BUT in terms of what was expected if they had lost that final stand in #54, yes. I mean, Jake’s parents were taken (his dad appeared as a Controller in #41. Rachel would have been out of the scene (obviously incapacitated to morph in #41). Cassie may have found luck in some sort of reputation the Yeerk-Peace Movement built for her and then became a voluntary resistant for the YPM (as shown in #41). Marco and Ax could have been taken down. While Jake and Tobias could somehow have escaped. BUT Jake was meant to have one of them slugs in his head in #41, too. So, what gives?!
Don’t think this is probable.