So in the Morse Code there are two small bits: SOS which is the same whichever way you read it. Then there’s a . – . – – . – which can be read as RQ or YR depending upon your orientation.
Typically folks accept this to say “RQ”.
We can’t just believe everything we read online… we need some sort of logical reason to pick RQ over YR.
It’s not definitive proof but go to either www.voynich.net/Kryptos or my Morse Code translation and take a look at those pictures one more time. The only evidence we have is what is really carved in front of the CIA, what James Sanborn did with the rest of the Morse Code phrases. Each phrase is in the same orientation, the correct perspective to read it is with the rock layer on the left and to read the Morse Code from left to right. Think of it as the Morse Code leaking out from underneath the rocks (not seeping back in).
So if we see this with every other phrase, is it safe to assume the same with the questionable code?
Probably, we have to make a choice one way or the other and the best we can do is make an educated guess.
From what I see in the pictures and how the rest of the Morse Code translates then it is “RQ”.
Kryptos - Beyond K4 
YR, RQ
They’re both useless as far as I’m concerned
I’m only just now trying to take in the Morse code subject matter. This would be a bias based on my findings, but I’d like to point out that my take on the X and Q found at the front and back end of the “Can you see anything” phrase in K3 is Sanborn’s way of suggesting a keyword that starts with Q and ends with X. Caesar shifted, Q/R and X/Y. Could the Morse code “RQ” be the primitive insight needed to suggest a Caesar shift?
Perhaps each of the Morse segments offer an insight into each step of the puzzle. All those E’s suggest to me a background space that is all E’s and like a palimpsest, some other letters are written instead to form those new words. Is the order of the Morse important, that is does the layout suggest the E’s portion comes first and the last part involves SOS followed by RQ?