Well, I would find it really strange NOT having the pad stack approach

It's so much easier to define a pad stack once and never worry about it again. And, as nctnico said, it's very easy to modify multiple items and to be consistent.
Usually a CAD tool that works this way also does the same thing with track widths, text styles and so forth. One big advantage is that you can define templates where everything is pre-defined. I have a "standard" and a "high density" template, for example. The standard template focuses on low cost, i. e. having track widths and via dimensions (drill size and annular ring) and a lot of other stuff that cause no extra cost with 99% of all fabricators.
And in my CAD tool I also can change properties of a single via that has been placed already. In this case the tool just creates a new pad stack with those parameters (if there doesn't exist a pad stack that matches).
However, I never heard about defining such things in an extra tool. That would indeed be a little weird, I guess.