When creating the Physics feature, I evaluated several different physics engines to use. These were evaluated on features, ease in integrating with Hype, performance, file size/footprint, developer activity/community, and licensing. Matter.js seemed to hit the sweet spot on all of these aspects, and it continues to grow and add even more features I hope to take advantage of and expose to developers using Hype.
Hype 3.5 does now expose a limited getter/setter API that allows for manipulations such as changing the position and rotation of elements. Theoretically if you wanted you could use your own physics engine and call into Hype's APIs to manipulate elements if you wanted. (Though at this point I'd probably question why you're using Hype instead of pure JS).