My scenario is connecting terminal emulators to getty or u-boot, which I think is a common one. A blip of line noise when plugging in would be barely considered an annoyance, easily cleared by pressing Backspace.
But yes, if someone happens to be using their serial line for some kind of sensitive signaling, then I would agree that choosing a more isolated connector (or just avoiding hotplug) would make sense.
Thing is, for a serial TTL connector to become ubiquitous, it needs to cover at least something like 99% of scenarios. Or maybe 95%. 3.5mm TRS ain't that, and thus just increases general diversity in connectors.
There's a small risk of CPUs and I/O pins getting fried if GND levels aren't equalized first and instead that equalizing force would go through those pins. One could argue that it's hardware designer's responsibility to save users from such things, but then again, using a better connector than TRS can be one of them.