I'll give one example (as it's one I was personally invested in). Doing a barrier in non-uniform control flow is wildly unsafe undefined behavior (I've had it reboot my computer, and it's easy to believe it could be exploited by malicious actors). To make these barriers safe WebGPU does a "uniformity analysis." However, that in turn required adding uniform broadcast intrinsic to the shader language, otherwise a class of algorithms would be impossible to express.
As I say, it's plausible this kind of work could have been done as extensions to WebGL, but I think the end result would have been a lot less compelling than what we have now.