I've been transmuting Primal Earth to Water every day now for 6 weeks and the time in which I transmute has changed by one hour. (First thing I do when I get to work) So yea, I do transmute and knocking the timer back an hour nets me one extra transmute every 24 days. You can try to justify it all you want but in all actuality knocking the timer down by an hour is pointless.
Clearly then, this change is not intended to help you, or people like you who manage their transmutes with extreme precision. Rather, it is aimed at people who are a touch more casual about it and do it "around" the time the transmute timer is up, as this means we won't suffer from a gradual timer creep as our transmute slips later and later in the day.
I personally thought it was an extremely elegant change: this wasn't meant to vastly improve the quantity of transmutes - as you say, it barely changes the real volume of transmutes going on - but greatly increases the convenince of the system for those who don't care to manage it to within a few minutes every day. Very far from pointless for many people.