The trouble with the multiple select is that you have to use it usually when that's what the control is. Users who don't know to control-click can do things like moving files one at a time in the OS, but rarely (never?) is an OS showing you a control like that that makes you use ctrl-click to use it at all, vs. a list of checkboxes or whatever, or contexts like selecting files where you usually can accomplish your goal piecemeal.

I agree that the feature/appearance/accessibility inconsistency you get from reimplementing the controls is a problem, but I think the right way to fix it is to raise that common floor of what the web platform provides. People want, e.g., comboboxes, they've been around forever in UI toolkits, but the web's standard answer for them is still pretty terrible, so it's no surprise that people reach for the libraries that replace the whole thing.