Most users either don't have such strong opinions about their scroll bars, or would prefer it looks coherent with the application, or OS-native (your preference). But I can almost guarantee the larger group of non-technical users will have never thought about the styling of their scrollbars for more than a few seconds.
Also in terms of accessibility, so long as they're doing CSS-only changes, and the bar is sized compliant and has proper focus states, assistive technology won't care.