This Atom Editor package draws indent guide more correctly and understandably.
You can change the color of guides by adding styles to your stylesheet, such as the following:
.indent-guide-improved {background-color: gray;&.indent-guide-stack {background-color: cyan;&.indent-guide-active {background-color: blue;}}}
Good catch. Let us know what about this package looks wrong to you, and we'll investigate right away.