The yields are already better than what is typically found, and there are also already going to be plenty of special yields like gold deposits available. I do agree that by the time you can claim them, the settling part of the game has become somewhat pointless. It's kind of similar to colonizing Orion back in MOO2. The nice thing that game offered was that besides just a really nice planet, you also received several unique techs for clearing the guardian.

So, maybe make the yields slightly better, plus whomever defeats the Boss gets a shiny new level 9 champion on top of what is already rewarded.

i think i got an artifact I could use to give a bonus to one of my existing cities (like a growth bonus or something).  but yeah, the tile yields should be better.