It actually simply used a different kind of a logic. Instead of viewing them as 3 separate rows of runes, the client had a set of 9 runes and you would pick A and B from the 9 runes. It felt wonky if you happened to misclick on a rune when you were clicking rune B, but because they weren't viewed as 3 rows but just 9 separate runes, only changing rune B would allow you to only ever change rune B.

Right now the same logic applies in that if you pick rune A from row 1 and rune B from row 2, if you want to change your rune B to a row 3 rune and go to click on a rune on row 3, it'll change you rune A to the row 3 rune because it has no way of knowing whether you want to change rune A or rune B to the row 3 rune.

However, the system being changed from 9 separate runes where you always have to switch A-B-A-B-A-B to a system where they are handled as rows makes it feel a bit more intuitive, but I can definitely understand the logic behind the old system too.