Compared to what ?
Two holes are better than one.
If you can get the holes bigger, the bigger the better.
Personally, if I had the choice between having two holes and having expansion, I will take the two holes. If there is a way to get both, I will take both. One obvious way to do that is to use a larger caliber from the get go: I took advantage of that from the beginning.
In the example mentioned, we have two 95 grain bullets traveling at 1000 fps. One completely penetrates and leaves at the speed of 500 fps. The other bullet stays within the body. There really isn't enough information to make any real judgement, but it sounds to me like the first bullet would be the better one.
First of all, there is not enough "energy" involved to make it a factor. We don't know if the first bullet disapated all it's energy on something like the sternum and never reached any vital organs. We don't know if the bullet penetrated two inches and petered out. We don't know if the bullet completely fragmented on impact and only did minor flesh damage.
The second bullet gave us complete penetration. That means there are two holes and everything in between those two holes has a hole in it. Everything between those two holes is bleeding.
Expansion is nice. Penetration is essential. Both is better, but if you have to make a choice, penetration is essential, expansion is icing on the cake. It doesn't matter (within reason) how much the bullet expands if it doesn't reach the vitals and put a hole in them.
There is no rocket science here. There are no magical properties involved. People dying from penetrating trauma is nothing new. The way a hangun bullet kills and the way a spear, or knife, or sword kill is the same as it has been since the dawn of time. You have to put a hole through the vital organs. You want bleeding. More bleeding is better. You want air to enter the chest cavity. More air is better.