It means that the framework makes certain choices and trade-offs, and doesn't allow the developer using it a choice in those matters.
I never took "opinionated" software as "no configuration". For me it's always been "custom defaults". It might provide some configuration, it might not, but what makes it opinionated is the fact that the defaults are not generally applicable, but rather tailored for a specific use case.
That said, I think it'd be really difficult to work around Elder.js' opinions.
It allowed for highly complex scenes, great static lighting and short loading times but it lacked in detail and dynamic elements.