In rugby most people (apart from Americans, in my experience) think kicking is better than receiving.
That's interesting and I'm happy to accept it.
So what we are effectively saying to the captain that loses the toss is "mate, the other skipper has chosen an end. What we could do is give you the option of kick or receive, however, experience tells us that you'd probably rather kick, so we'll make that decision for you".
Here's an analogy (I like analogies):
You have 2 children, Billy & Tilly. You say to them "children, we have 2 choices to make, each of which has 2 outcomes".
"Choice 1 is whether we go to the park on Friday or Saturday. Choice 2 is whether we play football or cricket once we are at the park".
"Now, I'm going to toss a coin. Tilly, you call heads or tails to see who gets first choice".
"Now here's where the fun starts, children. If the winner of the toss chooses that we go to the park on Friday then the other will choose whether we play football or cricket".
"BUT, if the winner of the toss really wants to play cricket, then they can choose cricket and we will automatically go to the park on Saturday".
"what do you mean 'that makes no sense'? We've been doing it this way since 1871!"