It gets confusing, yes. It shows that they switched design ideas in the middle of the development - from straight up VN with choices to this sandboxy thing. It feels tacked on and it really has a bad UX (User Experience), as the sandbox is confusing and not easy to use.
Having half of the options tied to some random items on a desk in one room (without even decent tooltips) and still having to click through rooms and areas without a feel for what is possible, what is happening when and where is getting tiresome quickly .
Personally I would prefer to return to VN mode, as it seems perfectly sufficient for the kind of story this had been so far. But if there truly needs to be be a sandbox for some reason (is there a strategy part planned? A kingdom simulation? Anything?), then the sandbox needs to be simplified, streamlined and much more information be displayed. Everything needs to be controlled from a single view (with maybe a few sub menus if really necessary), all pertinent info must be easily accessible and the player needs to be much better guided through the whole thing.
Also the whole game would need a rework in that case as this is not a seemless presentation. Having, what, half an hour to an hour of "prologue" that is a completely different kind of game before starting some kind of "sexy Crusader Kings" or whatever the plan is, wont really work out.