I'm pretty sure it was an opt-in thing for individual programs, if an app didn't intentionally use it they kept the old look.

I've always thought that it's a bit of an undocumented and slightly forgotten bit of Windows 3.1, most things on the internet only show the flat style. I guess people doing retro things often only mess around a bit with the base OS, and don't really install things like Office 4.x on top of it.