It's just the way the thing has developed, it started out purple, but certain users did not like that, felt purple did not represent their quadrant, which is where yellow came from.

Now they're kinda interchangeable, but on r/PCM the running joke is that purple is for people who don't like age of consent laws

Okay, this seems like the opportune moment for me to bring up something minor that bugs me.
AuthRight has blue.
AuthLeft has red.
LibLeft has green.
Centrists have grey.
Why does nobody agree whether LibRight has purple or yellow? I swear I've seen an equal number of each, and if you can't connect your ideology to a color, then that color does not do a good enough job of representing you.