I have a simple server rack I use as a Cisco networking lab. Part of this lab includes four desktop PCs running CentOS 7, via a KVM switch.

The PCs only have Display Port out, while the KVM is VGA, so there are DP to DSUB adapter cables in play. As a result of this mess, my maximum native resolution is 1024x768. If I set the resolution to this via the graphical configuration tool, the Gnome toolbar gets cut off, and the system thinks there's useable desktop space off the edge of the screens. If I use `xrandr --outpid DP2 --mode 1024x768` everything works correctly, until the next reboot.

What's the difference between using the gui and using xrandr, and how do I make it work persistently short of just shoving the command into my .bashrc file?

Edit: I should probably mention. All four systems behave the same way. Something about CentOS 7 and this hardware is interacting in a way to make this a consistent behavior. The exact hardware:
PCx4: https://www.amazon.com/gp/product/B01N4S6NC4/
KVM: https://www.amazon.com/gp/product/B003HO8NWS
Console: https://www.amazon.com/gp/product/B00VPK5L9E

Somehow, using xrandr to update the display, then opening the GUI tool and hitting "Cancel" seems to both work and make the change permanent.

I do not understand why, and this sits poorly with me, but it works. So I'll take it.

If someone can explain to me how/why this worked, I'm all ears.

Putting the xrandr command in a global startup script worksforme, and should for you. 1024x768 can also be forced globally via minimalist /etc/X11/xorg.conf*. With most Intel gfxchips, video=1024x768 (or equivalent Grub2 video mode setup) on the bootloader's cmdline works equally well if not overridden by xorg.conf* or xrandr or a DE's screen configuration.