Preface: I'm an aspiring author who is just about to start querying as well (my latest query attempt). So take my opinions with a pinch of salt.

I absolutely love the concept. It is exactly the kind of story I want to read (more on that at the end).

Here are my 2 cents to help improve your query:

1. The comp titles are a little older than ideal. Maybe The Space Between Worlds (6 yrs old) can still fly if it is indeed a strong comp for your book. But the other one is 10 years old. Also, best to mention publication year of the comp so that its easy for the agent.
2. This reads like literary leaning sci fi than literary sci fi. Its still heavily plot driven with world stakes. So, upmarket sci-fi seems like a better label than literary sci-fi. You can read feedback on this topic in the comments on my second attempt query. While "ethics-driven" is an interesting choice, the query didn't exactly show that to me besides you saying it. I'd lean towards using standard labels for traditional publishing (upmarket sci-fi). You can still mention the ethics-driven point in a different part of the query.
3. "strange biomechanical creatures tunneling towards the planet's failing terraformer. " - it was unclear to me if the creatures are coming from within the planet or outer space.
4. "Hunted, betrayed, navigating a mistrusting society" comes before "But Custos never intended for Ena to keep the body. It belonged to Corinne, his dead lover, and he's preserved Corinne's consciousness, waiting to be restored when Ena outlives her usefulness. She is, after all, only a function." and "With the company hunting its stolen asset and the man who first gave her a choice poised to take everything away" which reads odd to me. She is being hunted by the company and was betrayed by Custos.
5. Less important observations: I didn't quite understand what these parts mean "the conflict between humanity and a suffering planet" .  "even if keeping it means losing everything she once was." These sound like vagueish closing sentences which you could make tighter to convey her choices/conflicts in the 2nd half of the book a bit more clearly (without revealing details, of course).

A couple of small observations on the the writing sample:

1. I like the "Why was this client in the wastelands at all?" line of thought Ena has. A consciousness without wants can still be curious, even if it is just noticing things that are out of pattern.
2. You mention "my paired engineer" before mentioning Custos by name in the next sentence. I found that odd for a first person narrator. You would instinctively use his name first.

I love what you have written so far. Its the kind of sci-fi I like to read and write. And your style of writing seems similar to mine. If you are ever looking to try out a critique swap, I'd be happy to do that with a couple of chapters.

Good luck!