I suspect in some ways it's down to that magic ingredient of having a talent for such things. But I'm sure that shit can be developed and learnt though.
Listening to something like Logos' Lp compared to his previous Ep, you can hear his development in refining his sound and reducing it down to the essentials. Working with space whilst keeping a groove going is a real feat imho and he does it better than most. It's well worth going through the tunes that you really like and deconstructing them in some way, see how they do 'it', then trying to transfer that knowledge to your own work.
I remember reading an interview with Rick Rubin, talking about him and Kanye going through the final production for Yeezus. He said it was all about making it "edgy and minimal and hard", and more about taking out everything vaguely superfluous. I often think about that when I'm working on stuff. If you start with a basic loop with a solid beat, then deconstruct it, dub it out somewhat. If certain elements can't stand up on there own, maybe they're not strong enough. If everything can, then you know you've got something good that you can edit, or build, from. That's kind of how I think about it at the moment. I couldn't sit down and think about it as a whole and write something straight minimal, cause I don't have that skill yet.
The other people I think about when it comes to making minimal music with a serious groove to it are the 90s dancehall producers. Guys like Steelie And Cleavie who were used to devoting hours to tuning instruments and getting drums miked correctly etc, would now spend that time and devote that level of attention to going through the drum samples in their SP1200 or DX and making sure they were constructed & tuned exactly how they wanted them. And that the kit, as a whole, worked together like a real drum kit would. It's that kind of attention to the details that pushes a sound up a level imho. Especially if you're making something quiet minimal, each part needs to be considered and strong.
I may be kinda waffling now.
On a more practical note, what vst do you use to make those nice glassy square wave synths? I've yet to find one I can really work with. I really like the functionality of Operator in Abelton, but the final results can be a little weedy compared to others.