90% sure reddit doesn't do this by default and it's a style choice by certain subreddits.
On larger threads idk how impactful this would be. you'd scroll so far it'd be hard to tell anyways. On smaller threads it's already easy to see who replied to who so it's not really necessary.
larger threads where replies have near entire threads in between child replies to the OP would require scrolling regardless of alternating color coding.
What is really needed for better readability is small lines like reddit does between replies
[http://i.imgur.com/bRunD1r.png] (note: color coding would create this line, however it'd be a pain to do color coding alternating child posts on cys)
In the end, both would technically work depending on how implimented. The reason coloring likely would be more of a pain in the ass is the .forum-message div doesn't go all the way down
[http://i.imgur.com/SfpsjXR.png]; if it did then alternating the colors of divs would also outline their child replies - but it doesn't. That would need to change for color coding posts to be a viable option for improving thread readability.