That's true. It could've completely done away with it, and I doubt many would've missed it. But it at least skirted the line between neat throwback and clear rehash instead of crossing over it. It took the iconic boss rush, spread it out, and gave it different contexts. But now that you bring it up, I don't think even the straight-up boss rush needed to come back regardless how it's rearranged.
What would've been a better way to design or envision final stages for Mega Man X, assuming boss refights were off the table? The prevailing notion I'm seeing about why boss refights exist was for you to use the right weapons on all the right bosses; more to the point, it's to beat them to a pulp better than your first fight with them. I've always felt like these refights were kinda filler material, but I never questioned it because it was tradition and just rolled with it.
So instead of just replacing the old 8 bosses with 8 new placeholder bosses (where you'd have to guess their weaknesses all over again), we can make a slight variation by having you fight 2 vs 1 matches instead of 1 on 1s. They're the same bosses with the same weaknesses, but now it's a completely different fight owing to two factors: now you're outnumbered, and now the terrain is different, making the stakes much higher. So, like, what if the boss room checkpoints were better designed to seem like they were actually trying to stop you from progressing? Like timed death traps during the match or hazardous industrial machinery adding tension in the background? These could play out more like special scenario thrillers instead of a bland sequence of boss fights. Better still, your choice of weapons could manipulate the environment to your advantage and buy you time or bring the match to a sudden victory for you.