My testing is specifically limited to Xaku's "The Vast Untime" ability since that's where I first noticed it on PC. When doing RJ missions and going to pilot the RJ, the ability timer on the screen effectively freezes, but the timer keeps going in the background.
Explanation:
Cast The Vast Untime. Counter starts (for example) 30 and starts counting down.
Now let's say you in to pilot the RJ at time 25 for 10 seconds. When you hop on and when you hop off, the player sees 25 at both points, but when you hop off, the ability will run out in 15 seconds (when it says 10 on the screen).
Again, I have only tested this on Xaku, but I can imagine that this may translate to other WFs as well.