Cannot see the double quote mark when the text is highlighted.

[stevemao]

See the double quote after red is very hard to see. Maybe make the highlighted area a bit smaller for html?

[stevemao]

In fact, it would be better if the highlighted area is below other texts.

[abe33]

For the double quote, you can prevent that by changing the styles of the markers to remove the margins and paddings.

For the marker z-index, putting it behind text make it impossible to use a contrast color for the text, so if the marker color is close to the editor text color it becomes unreadable.

[stevemao]

Can the highlighted texts have the highest z-index, then the markers, and the rest texts have the lowest?

It might be handy if you expose settings of the styles in Atom?

[abe33]

Can the highlighted texts have the highest z-index, then the markers, and the rest texts have the lowest?

Unfortunately no, by doing that the contrast text would overlay above the editor's text, resulting in a thin border around the text as the antialiasing may be render differently whether the text is white or black.

In the next version (namely abe33/atom-pigments) there's a setting for the type of markers (background, outline, underline or dots). But as long as there's no API in atom to decorate a part of the text so that one can change the text color at a specific place without creating an overlay I won't be able to use the decoration API.