Don't be so harsh on developers! It's not that they're fear-mongers, it's just that they are not the "general population". Most freeware authors write software for
themselves, and then make it available to anyone else who might have the same needs. It's up to you to decide if you share those needs.
Maybe it's true that 99% of people should never defragment, for example. I certainly don't advocate it for the average Joe, but it takes a lot to ensure that fragmentation is not a problem for
me.
I'm sure there are cases when running cron scripts manually is useful. The truth is, the geekiest geeks know how to take care of
their machines better than any OS ever could. What makes sense for one person may not make sense for most people, and what makes sense for most people rarely makes sense for
everyone.
There's an old saying: "It's better to know nothing than only a little." (Or something like that.) It often applies to computers.
Having said that, I really don't know of any reasons to run cron scripts manually. I'm sure there are some, but I imagine they're not relevant to the general population.
As for repairing permission....well, it can't hurt. 99% of the time it won't make a difference, but do you want to fall under that other 1%? It's easy enough to do, so I play it safe (at least when I remember, which is rarely). Same thing with using "combo" updaters. (And the same reason I look both ways before crossing a street even when I have the "Walk" sign.

) A 1% chance of disaster is enough to make me go a liiittle out of my way.