The short answer is that it doesn't really matter.
The "protected area" is not important for photography; I'm not aware of any camera that uses it. This area is theoretically used for user-hostile copy protection and is not really for your benefit in any case. When using your camera to store photos, you can just ignore it.
The concern about less than optimal performance is unlikely to be relevant with any modern operating system (or camera). I think the main concern is that the OS may do a "full format", causing unnecessary writes. Since this is terribly slow on any storage device of the capacities we use these days, every OS uses the better-for-flash quick formatting anyway. There's more on this under How often should memory cards be formatted?
As answers to that question note, camera makers usually recommend formatting in-camera rather than with a computer. There are several reasons for this:
- A user could format the card with an incompatible filesystem, like NTFS or HFS. This would cause confused users and expensive tech-support calls. Better to just say "do it in the camera".
- Very unlikely, but a bug in some OS's FAT implementation or in the camera's own firmware could conflict. Keeping it all in-camera is safer here (but I've never heard of this really happening — the filesystem format is simple and well understood).
- Formatting in-camera causes the DCIM folder structure to be created — but as this happens when you write a photo if it's not there already, this is unimportant.
If you understand all this, there's absolutely no harm in formatting the card on your computer, with the special SD Card Association firmware or with the OS's own tools. If you don't, use the camera's own formatting to be safe.