Unity describes this tie-up as a "strategic collaboration" that aims to offer an "optimal authoring solution" for Microsoft's HoloLens technology. The touted authoring solutions include tools customised specifically to leverage the AR aspect of HoloLens.
For example, one of the tools showcased at the event allows developers to anchor virtual holographic objects onto those in the real world. A good illustration of this implementation would be the ability to play Real-Time Strategy games using the HoloLens, with a real world coffee table serving as the battlefield. This will allow developers to achieve a tighter and more meaningful integration of the HoloLens' AR aspect into video games.
Techcrunch points out that the low-cost, PC-centric nature and versatility of the Unity engine also makes it the backbone of choice for a majority of Oculus Rift game developers. This, when combined with the relatively open nature and ethos of the Unity engine, means that the deal between Microsoft and Unity Technologies doesn't seem to entail much in terms of exclusivity for Microsoft.