You're looking for a percentage I assume? Seeing as you're talking about a hypothetical Type-IV+ civilization, you could get 100% of the universe to be livable if you had the right resources. Gravity is determined by the interaction of two sources of mass. The Earth has a certain amount of mass spread across a certain volume of space that we get the gravity we have. By making a super-light (but durable) metal or metal-alloy, this could literally be a series of sheets spread across the universe that people walk on and take escalators or lifts to travel between them. Additionally, this Civilization would already have black holes under their control and command as is a requirement of being Type-III, so to be Type-IV+ it's a given that they could make the black holes livable as well in some way, shape, or form. By your supposition that this Civilization can create matter and energy out of nothing, you are effectively confirming the existence of white holes in your universe (something which is still only hypothetical in our own world). Worst case scenario, the black holes get filled with white holes and aside from maybe some minor gravitational distortions (depending on how good the patch-job is), you have livable universe. If you can manage to live physically inside the black holes, though, you could argue that's an infinite source of livable space independent of our universe at large, meaning the answer is technically 100%+.
The important thing to consider is this: living space is about perspective. Each family could own their own galaxy in this circumstance and that is all their living space, even if they never actually use it all, the black hole at its center being used as a furnace to power their galactic mega-structure. At the same time, you could view 3 cubic meters as the extent of one's living space, and as long as everyone has these fancy matter creators, anywhere in the universe aside from black holes (and even then) becomes potential living space because you can just eliminate whatever exists that you don't want to exist. You can create anything too, so with that there are no limits. Make material that is perfect in thickness, density, and durability... and you have now created a universe of nothing but apartments.
It's worth noting that unless you're writing an erotica, this would not be a good universe to have as a basis. Ignoring the fact that by now, purely biological humanity would be non-existent... These people would suffer from incredible boredom. In a world where you can create physically everything, which technically includes other life, there is no need to work, and every game gets boring after a while... eventually these people will be reliant on fulfilling only one primal instinct if they are still biological life at all: their instinct to reproduce. Since they can also CREATE their ideal partner(s) thanks to this technology being able to create matter and the fact being able to create/manipulate neural pathways would be child's play by this point in the future... Dating won't even be a necessity anymore, not they'd feel a need to go through that process anyways since it'd all be about the act, not the symbology involved with eventual marriage or a monogamous relationship. The reproductive process is essentially all they will be doing because nothing else in the universe will have value, and even the value of reproducing in and of itself will be null, making the value solely in the act, not the outcome. (You could also argue that a terrorist cell might form out of boredom that attempts to destroy these matter creators... but anyone with a brain would know the machines would just be built again or they'd be remade faster than they could be destroyed; therefore, making the act of terrorism pointless in-and-of itself, and anything they do could just be countered by these machines anyways meaning it is doubly-pointless.)
Solution: Limit the technology's omnipotence. The fact it can create on-command is extremely overpowered and is enough to make this universe of 100% livable space. The issue is, once you reach Type-IV, it doesn't matter what you say: This civilization has domain over the universe like we have over small patches of dirt. While we can terraform local areas, they could do so to the entire universe. Push any beyond that, and you're looking at a Civilization that has succeeded in multi-universal manipulation. It's just an exponential growth system. Stick to Type-III and lower. It avoids any of these issues.