It isn't just about resources they are giving up, but the fact that now you have a political situation on your hands with the next inheritor. Who will get a chance to develop those resources. That was the real point. The planets you wanted may be weak but now a STRONG (one hopes) AI has them and will have a chance to build them up. And you may not be immediately ready to go to war with them.
And nah you missed the other point- surrendering earlier means more resources to work with.
There will not be any significant changes to the political situation unless one faction surrenders with most of its power rating intact, which is not going to happen if it had to surrender to begin with given the AI behavior. The power rating that one faction gains from the merging is not going to be enough to suddenly change the status quo unless that faction already hated you enough and you were already significantly behind on power rating.
The change you are suggesting is also extremely situational because if you are the strongest faction or if it went to an AI that actually likes you, then nothing is going to change except now there is one less faction to deal with. That is not to mention that if you just happen to be the strongest faction, then it would make even less difference because you would steamroll them all the same, since this game does not count your potential production capability or technology as much as it should.
The real point is that it will not make the game any harder, only more predictable and easier to manipulate in your favor. Since having a high power rating holds so much weight, you just need to make sure you are on friendly terms with the most powerful faction or artificially make a faction stronger by giving them free stuff.