Not related to HiDPI, but looking at the picture of his monitor setup: From an ergonomics standpoint (i.e. the health of your neck), the upper edge of your monitor shouldn't be higher than your eye level. Looking straight or looking down is fine. Thus the monitor on the left is probably not very ergonomic.
Author here: you’re absolutely right. My previous vertical monitor was a lot shorter; this one has definitely not been great for my neck. I’ll probably switch it back to horizontal at some point.
I find having a vertical 24" monitor to be super useful, especially for reading typical PDF files as an entire page fits nicely on the screen.
My vertical monitor is a bit closer to the desk, and the horizontal monitor is much higher than yours, about 7.5" above the desk. The bottom edges are not aligned; the vertical monitor bottom edge is about 5" below the bottom of the horizontal monitor, and its top edge is about 3" above the top of the horizontal monitor.
The top of horizontal monitor is just below my eye height. So the top of the vertical one is a couple of inches above that, but this is not a problem as I don't spend much time looking at the very top of that monitor.
Each monitor is tilted separately. The horizontal one is tilted back only slightly; the vertical one tilted more. So the center of each monitor is perpendicular to my line of sight.
At the moment I'm using the two monitors with a Linux desktop, but sometimes I connect them both to a ThinkPad for a three-monitor setup with the ThinkPad's display and keyboard. When I do this, I raise the horizontal monitor up another inch so the ThinkPad display tucks in underneath it.
With your horizontal monitor sitting so close to the desk, I have to wonder if your seating position may be too low? Are your forearms horizontal when typing? (Forgive me if I'm being nosy or presumptuous, just curious.)
One related tip for anyone reading this, regardless of your monitor arrangement: if you wear glasses, do not use progressive lenses at your computer. Instead, get a pair of single vision lenses with a fairly tall aspect ratio so they let you see the entire screen(s) without tilting your head back. Don't ask your optometrist for a "reading" prescription - that tends to be about a 16" distance, and your monitors are probably farther from your eyes than that. Measure the distance from your eyes to the monitors and get single vision lenses made for that distance.