I have 3 monitors attached to my PC. And it seems that, just like Gnome, when disabling/re-enabling a monitor, its customised position gets forgotten. That is, I have to drag the monitor and re-arrange them. In the Display Configuration, to switch to the setting what I want, I have to change multiple things and I have to confirm it each time.
Instead of letting the user change one setting at a time within the GUI, why can’t it have a feature to save the current configuration as a preset, and let the user switch between presets. It’s basically the same as manually changing values within the GUI, but doing at once. To me, this seems like an easy feature to implement (if the person already knows how to programme KDE’s Display Configuratioin GUI, which I don’t). Is my assessment wrong, and this would be actually very difficult to create?
Also, the users presets can be shown in the Meta + P pop-up menu, instead of those mostly useless default items.
What you’re describing sounds like a fixable bug. In general it’s best to fix bugs rather than add configurability to let people find their own workarounds for them.
Are you using Plasma 5 or 6? And are you on Wayland or X11?
Wayland Plasma 6 on Arch. Gnome’s Settings never remembers the monitor position in this scenario, but KDE’s system settings seemed to restore the position when I enabled it right after disabling it. But this time, I enabled it a lot later, and the monitor position was not remembered (back to the default position which is different than the physical position).
Maybe using 3 monitors is a rare case, but there are situations where I need only 1, 2 or all 3 monitors enabled (e.g., only 1 for watching video, 2 for general work, 3 for special work), so manually enabling/disabling monitors and changing the arrangement isn’t convenient. If not preset, does the KDE system settings let me programmatically change display configuration settings (all the things that I can do on the GUI), so that I could automate the changes?
Yes, you can automate screen setup stuff using kscreen-doctor. But really we should fix the bug. 
What kind of GPU (or GPUs) is/are the screens plugged into, and what are their connection methods?
KWin remembers the position independently of the output being enabled or disabled, so if you enable the display with kscreen-doctor instead of the GUI, the output should already get placed in the correct spot.
If the GUI puts a newly-enabled output in a different place, that’s something that can and should be fixable in KScreen
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I think I have found the step to reproduce the problem. Physically Dell is on the left and Samsung is on the right. But the GPU thinks Samsung is 1 and Dell is 2, so by default, the OS shows them in a wrong order. At the beginning of the video, I moved Dell to the left and applied (this is the typical state). Then, I disabled Dell. Then, I re-enable Dell. Dell appears on the correct position (left), but I forgot to click “Keep”. Then, Dell got disabled again, but the GUI still showed “Enabled” checked for Dell. I changed device and now Dell was shown not enabled. This time, if I enable Dell, it appears on the wrong position (right, which is the hardware default). Is this a bug, or an intended behaviour?
I recorded the steps above in WebM, but this site did not allow me to embed the recording here or even adding link to Imgur, where I uploaded the WebM. If you need to see the screen recording, please let me know how I can give it to you.