Oh yeah, while I haven't read the source directly in years, it is much changed. I was referencing 2004, only six months or so after iRO officially came out of beta. To say it improved since then is an understatement. Based on what I last knew about the scripting capabilities of the Gravity server implementation (circa 2008), I can safely say that eAthena eventually came to provide an easier model for rudimentary content creation and management than the official software.
Never mind security. Trying to wrap your head around the code behind why opening a dialog via item X and performing client action Y on the keyboard would bypass what should have been a server-side security check for a very important game mechanic was a lesson in all sorts of SE principles. Unnecessary coupling and spooky action at a distance, for starters. Repeat this a hundred times and mix in a handful of SQL injection points, plus some fundamental disagreements in how and when the game's content assumed characters would appear on a new map, versus how and when the official servers actually worked.
I am curious if and how eAthena eventually deviated from some of the idiosyncratic behavior of the official game servers.
From what I've heard in the years since I stopped playing, though, is that Gravity took the profits from their microtransaction e-store and managed to actually plow that money into improvements for the GM team's ability to meaningfully manage their servers and community. So my first paragraph likely applies only to a bygone era.