It depends on what price range of keycaps you are looking at. Every GMK set will come with options to do either the 1u x3 or 1.5u x2 setup you mention. Cheaper sets often only include 1.25u modifiers. I just built out my budget96 keyboard today and I chose the 1.5u x2 option to the right of the space bar. I think it looks better/cleaner.
TLDR: cheap sets won't cover either option. If a set covers 1 option, it will most likely cover the other.
Hope this helps. Might just want to look for keycaps and decide on the caps before you build.
Ah I see. This very much answers my question.
Unfortunately, my budget is not too high at the moment, especially considering how much I'm spending on the keyboard alone.
I guess I'm stuck with YMDK's default 96 options. Thankfully it's cheap at around 25-ish dollars. I suppose I'll get a better set once this cheap set wears down.
Since "a set covers 1 option, it will most likely cover the other" is the case, I'll just pick out the 3*1u. I personally use Win often, so it's gonna have to stay.
Thank you very much for the insight!