It seems that vega-embed will not work with some vega-lite config
that is offered with vl.compile(spec, {config}).  For instance, the default
mark color '#4c78a8' cannot be overridden with

vegaEmbed(el, vega-lite spec, {config: {mark: {fill: "#aaa"}}})

We can make it work by manually compiling with vl.compile(spec, {config}) 
before vega-embed.  Or we can also add the config in the vega-lite spec.