It's pretty easy to understand. Ultimate's roster was finalized in 2016. Sakurai didn't play Xenoblade 2 until 2017 or after - it was too late to add him to the base game.
Nintendo decided the DLC for Smash, not Sakurai. Nintendo must have felt they wanted to promote an upcoming Fire Emblem game when the DLC was decided on.
Maybe Nintendo suggest Rex as well but Sakurai said movement wise it wasn't possible, but Pyra/Mythra were.
http://www.nintendoworldreport.com/news/48860/sakurai-issues-statement-on-smash-ultimate-dlc-characters-selected-by-nintendo
Here Sakurai said the list of possible DLC characters was made entirely by Nintendo. Sakurai just told them whether a character was possible as a fighter. Beyond that who knows how much input he had.