I want to be optimistic, bit honestly this to me reads like the non-commital "thanks for your concern, we'll look into it" consumer service style non-answer.
I hope it ends up somewhere, but I can also see it remaining in their ticketing system for eternity.
I think the Steam Deck is a platform that devs are aware of, and I'm sure they don't want to alienate that segment of their sales. They also want to avoid negative reviews.BattlEye is also supported in other games on Linux, including native versions, so it shouldn't be a big deal to ensure its functionality.