I'd argue that Stranger Things 4 was the bigger IP than The Last of Us for HHN 32 (not saying that either house was "better", but ST4 definitely had the bigger hype and longest house wait times according to Thrilldata).
So Universal had 3 options:
1. Keep ST4 on the 6 house tour, without Last of Us.
2. Move ST4 to the 3 house tour, instead of Last of Us.
3. Keep all the big IP's on the same tour (6 or 3 house tour).
For my last point:
It's not surprising to me that Universal wanted to separate ST4 from Last of Us to get HHN fans to buy both tours. As for why Last of Us was delegated to the 3 house tour instead of ST4 (your original point), it's honestly a toss-up.