For me being able to set a custom focus limiter distance is hugely useful. At an airshow I can set the limiter to 100m and be sure that as I pan on a low flying aircraft it simply will not try to refocus on anything really close to the flight line that might get in the way. Having an older body with fewer AF options makes this even more important to me. So yes the custom options are pretty useful.
I am trained as an engineer and so realise that if you you want to have lenses with super accurate AF systems, that always work when shooting a silly small DoF's you have two choices. First you can pay through the nose for a system that is built to tolerances so high that no calibration will ever be necessary, at least for some, probably quite short, designed life cycle. This by the way is the option where the nifty fifty starts at around $1000 and prices go up from there. I actually doubt that this level of engineering would always work.
The second option is to build to a high enough standard of tolerance that 90% of your customers are unlikely to have any issues, even when mixing different combinations of lens and body. For the other 10%, although given the numbers of cameras Canon sells, it's probably really less than 1% that have issues, you can either simply charge them a fee to calibrate the lens to the specific body, since both the camera and lens are likely well inside the respective tolerances neither would be classed as a warranty repair individually. Or you can provide a system on the camera or lens to allow the user to do their own calibration at no additional cost to them.
Given that my personal circumstance mean that I can barely afford to buy even nice secondhand kit, option one would be a non starter. I would think that even the 1% would baulk at having to pay upwards of $1000 for a simple 50mm f/1.8 prime, and $10000 for the body. Just to ensure that the AF system would be exact every time on every body/lens combination possible. Having a system to take care of the very few times that there are actually tolerance combinations that produce visible problems makes much more sense for highly critical customers.