If you have 7 gems leftover from a purchase, you can convert X amount of gold into 3 gems and then convert the 10 gems into gold. This idea of "salami slicing" in GW2 is a myth.
Since they re-introduced the custom conversion rate, not only can you easily transfer any quantity of gems into gold, but specifying how many gems you want is far easier than it used to be. Rather than punching in a set amount of gold and seeing how much you get back, you just say how many gems you want. I actually find this system a lot more convenient; I just hated that it didn't have the custom conversion rate at first.
This is a non-issue.