People have been talking about the possibility of settlers stealing your stuff, so I've been wondering can you make a house that you'd have to jump to access (for example roof entrance and jump from adjacent structure) and might that stop settlers from entering it?

Why not have a house with a ladder and just remove it so nobody can enter but you?

Does not matter matter. the NPCs can show up on a forced respawn (from Fast travel or running in from beyond there spawn into game range anyplace and any level there is a nav-mesh including all settlement building floors and roofs

that's what I did. A little jump to keep them jerks off my lootz.