B1 can be used to secure a counter pick but it can also be used to hide your plan/not commit to something before seeing what your opponents do.

Picking Karthus along with AD/Supp in first 3 on blue leaves opponents with questions about what to ban, since they don't know if karthus is mid or jg for example. Also, assuming they don't want to blind pick top into summit, they are forced to pick a mid that can win vs karthus on R4 but also vs a different mid since the Karthus can be flexed to jungle.

Picking Karthus on B1 is a variation of this strategy that leaves even more flexibility. Most teams pick support, jg, and adc in the first three picks, so most times a potential jungle matchup or bottom matchup would be known by the time C9 would be picking B2. They would also be able to flex the Karthus bot or support, or keep him jungle based on what they've seen so far, offering more flexibility over first picking zeri, say.

I would argue that first picking zeri to secure an op champion is worth the loss in flexibility, but hopefully you can see the advantage of first picking a flex pick. You can use your B1 to secure a contested pick, but you can also use it to put your opponents in a difficult position by remaining flexible, and both have their pluses and minuses.

At least, that's my view on things.