The camera will remember the settings for each different lens model, and if you use a teleconverter or two it will remember the settings independently when they are fitted too. However, if you have half a dozen identical lenses - e.g. Canon 50/1.8 - you can't store different settings for each of the same type.
IMHO FoCal is worth the money if you have several combinations of lens/body and want the most effortless, quick and reliable method for calibrating them all. If you only have a couple of lenses and don't plan on a big expansion then maybe not. Since I have three bodies and nine lenses, making 25 possible combinations (The Ef-s lens I have won't fit two of the bodies) then it is a very useful tool.
More than just automating and simplifying calibration, it also highlights how consistent (or not) the AF performance of your gear is - something which might not be obvious with manual calibration and could throw a spanner in your efforts in some cases.
It has other features too, such as analysing the sharpest aperture for each body/lens combination, and more besides. It was released in January at version 1.0 and version 1.5 is on the way, having added more cameras, features and performance tweaks along the way. While on the 1.x release series the upgrades have all been free. When it moves to V2.x there will be an upgrade fee, but it's so good as it stands, in my experience, that I can't imagine what V2.x might bring that I would need or want.
Oh, and the licence will cover up to five bodies (serial numbers) and you are allowed 10 changes of registered serial number, so that should keep it future proofed for body upgrades for a bit, unless a new camera is released in the future which might require a full version upgrade rather than a point release.