SPOILIES!
It's Alluded That It's Been Tampered With A Bit When Arthur Says It Looks Kind Of Flat. If You Remember, Patience Souls Have Mind Magic, So What That Actually Is Was A Sort Of Minor Illusion Like In DND.
I Had A Discord Member Ask The Same Thing And They Also Asked If Nathan's Soul Was Hidden Too, To Which I Confirmed That It Wasn't, As They Both Broke Out Of Ferris Before They Were Transfered To The Facility Where The Doctors Can Carry Out Awakenings Away From The Public (The Same One From Chapter 3, At The Edge Of Town)
This Doesn't Mean Nathan Couldn't Get Tainted By Trauma Later And Have The Chance To Awaken If He Has The Mental Fortitude. Then Again, Arthur Wouldn't Have Been Able To Handle It Without You And That 'Other Version' Of Himself Telling Him To Fight.