Honestly, I don't think 99% of owners know the answer, including me.
My feelings are that the two bikes are identical except for the obvious differences.
I remember reading an official Yamaha blurb about the WR-250X (or, at least I think I remember reading it) saying the suspension came with different settings compared to the WR-250R.
Different settings can mean merely different compression and rebound clicker settings, and/or having the spring preload set at a different length.
If you want to ask somebody who has their nose inside the guts of these suspension parts, ask a reputable suspension shop guy like Travis from Go Race Suspension in VW.
He did my WR-250X shock, he says he knows much about these two models, and I wouldn't be surprised if he can give you an answer.