`/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.
The Linux kernel doesn't rely on the filesystem for swap files insuring no more overheard than swap partitions. It bypasses the filesystem and is told what blocks it can use, that's why some filesystems do not support swapfiles as there is additional plumbing to be done.
At one point in the past I used the default (or recommended) /boot size and got stuck a couple of years later juggling at updates to fit the boot files into the partition. I just use a monolithic partition per OS per disk now and swap files within that. Is that not good practice (for home systems)?