Is it possible to flag Settlement placements as personal?

Try setting up a bed on the second floor, deconstructing the stairs, and building a neighboring, unattached structure (or just a plain wooden staircase) that you can scale and use to jump over to your luxurious second floor bedroom.

Sorry Dogmeat, not THIS time. Find your own bed.

I've read that you can assign settlers to beds, so if you stay on top of which settlers you've assigned to which beds, you should be able to keep the people you've lovingly helped out of your bed.

Seems like Settlers can't handle fences either. Another easy option would likely be to simply put up a fence around your area with no gate. You may have the occasional issue with someone spawning inside the fence, but I don't believe I've ever seen a settler spawn inside a house other than the one with the initial workbench. You can jump the fence with ease, your settlers are stuck outside looking in longingly. Just make sure not to put a gate in it, because they WILL use that.

The easiest solution to this that I've found is to simply have a settlement without any settlers to serve as your own personal home base.

I've built out the Red Rocket station as a personal crafting, storage, and showcase area, and it's where I send my companions when I dismiss them. Meanwhile, I've built up Sanctuary as an actual settlement. Because the Red Rocket station is 'uninhabited', I have no issues with settlers taking my stuff or using my bed, and they are free to manage their own affairs in the village next door.

Unfortunately not. In fact, I have the distinct impression from the way Preston talks about Sanctuary that he doesn't really acknowledge that you were there first!