I think you're projecting a little here.
Rex was too late for the base game but Byleth had the right timing for DLC. They are two different things.
Sakurai didn't "sacrifice" anyone. He just made it so that people can dress their Miis up as popular costumes. If Nintendo wants Rex to be in the second pass, a Mii costume won't stop them.
I get the reasoning why Byleth is here
But i think for more casual viewers, if they watched the final direct, Sakurai states that Rex was too late to be on the roster (well at least base roster). Seeing Byleth make it in, who's game comes out over a year later make it in, and it doesn't feel too good, even if the reasoning is more complex and everything.
Plus Byleth themselves are very Controvisial newcomers. I know people that don't buy entire passes for characters they don't care about, and Byleth is that sort of character that would pose those strong reactions, so making Rex Costume by buying an entire $25 Season pass, that includes Byleth might not sit well with people.
And yeah i don't think Rex being a Mii Costume will automatically stop him from being playable...maybe. If he's not playable though, I do think they should make his Costume Purchasable desperately