`/home` should be separate from the system so you can reinstall it without trouble. Same for `/var` (or subdirectories) if you value the data of particular services. Other than that, the bootloader and EFI must be able to access certain directories like `/boot` and `/boot/efi`. As long as it works for your use cases, everything is alright.

Edit: A swap file has a little bit of overhead because of the underlying file system. But at the point you notice this, your system is pretty much frozen anyways.