If you don’t want to redo or edit the vanilla navmesh in the Skyrim SE Creation Kit, a simple workaround solution is to add a collision box and use that as a “navmesh cutter” instead. Here’s how. 
Drag in or select the object you wish to add a collision box for in the render window.
Turn on markers by having the render window active and pressing M.
While having your object selected, press the “Create a collision cube” button in the top menu of the Creation Kit; it’s a “C” inside a box.
If you can’t see the text explaining the top menu button presses, hover your mouse over the menu and click on it’s border to make the text appear, then re-select your object in the render window.
If necessary, resize the collision box by manipulating its arrows (click on the corresponding arrow).
Select the collision box and right click it to edit. Select “primitive” from the submenu, and change where it says collision layer to “L_Navcut”. Press the ok button.
To hide the collision box in the render window, press M.
Save your plugin.
Video version:
More on primitives here.
More on navcut here.
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