Everything on the tile will transfer, yes.
No, if you want a special place, you’ll have to use the transfer tool or the vehicle transfer method on the wiki.
Files downloaded from the internet may be harmful to your computer, yourself, your loved ones, baby dolphins, and the world as we know it.
Alternately, you could try deleting your maps folder while you’re in-game (make a backup) and then saving, and copying the new maps folder over to the new world, which should record only the overmap squares in your reality bubble. Probably. I don’t actually have any idea, but that sounds like a thing that should work.