I would play that A with 3 as well… although maybe 4, I’m not in front of the piano right now so can’t be sure…
But what I was going to say was, perhaps you could try just playing the lower C# and the A, with your chosen fingering, and see how it sounds and feels when you voice down the A…. The point of this would be to get a feel for it, and to hear it, as a way to maybe get closer to doing it when you’re playing all the notes.
Similarly, play just the RH part while focusing on quieting that A, and give your ear and your hand time and mental space to experience it.
Lastly, you might just try to bring out the upper C# more and give up on worrying about the A, hoping that, as you say, over time and practice, the A will become less prominent.
Oh btw, does your hand feel tight or does it feel hard to play the C# A C# chord? If so, it may just be that it will improve as your hand gets more comfortable with that shape.
Good luck, this is a beautiful piece!