If you're building a web app (say, via electron) as opposed to a site or document, using the system font stack will make that app fit into the desktop environment much better than Arial, Times New Roman and Courier New will.
What is being compared? Because to me it read like a question of choosing 'sans-serif' over 'ui-system-font-sans' or whatever in your CSS. Nothing more than that.
"System font stack" — which I took to mean the longish list of commonly known default fonts for a bunch of OSes brought up earlier in the thread — with a CSS value of "sans-serif".
There was no mention of direct use of Arial, Times New Roman or Courier that I could see, so I don't see why bring it up.