Rich Morris' Comics - YAFGC and The ComixBlog

I interpreted it as (1) reminding Arachne who she was speaking to and (2) that Arachne (being mortal) does not have the same point of view or thought processes as an immortal God.

Translation: Tread lightly, and don't presume you are smarter than an immortal or know all that there is to know about the situation.

(We all know what happens when your logic is impeccable, but Loth still hates you... )

Arachne also rubbed Lolth's nose in the fact that she was manipulated into making a big mistake. Lolth is prideful; she doesn't like being reminded of the fact that she has egg on her face -- to put it mildly -- and her letting Arachne live is a sign of how much she's impressed her.

But what if she is really smarter than the immortal being in question?

Extremely unlikely. In my game worlds, gods frequently suffer from information overload and miss important trees in the forest of information. Once their attention is drawn to the right trees, their intelligence and eons of experience (as well as divine powers) give them the edge. On the other hand, mortals, only have to worry about a very small section of the forest, and so in some cases can know its trees better than the god at first. This can give the impression that one is "smarter" because they figured out something "first", but it is a false impression. Similarly, if you were to physically punch a god in the arm "first", this does not automatically mean that you are "more powerful".

Lolth spent a lot of time binge drinking in drow form. It doesn't seem that she cares about that lots of information.

I think she just reminded Arachne than no matter how powerful or intelligent she is now she will in the end perish like everybody and end up in Lolth's Abyss for eternity. So there is no actual edge for her as long as she is mortal.

But will she, really? The Order of the Spider is still a big mystery. As its agent, Arachne is apparently above the law. Is she also above the state religion?
Let's face it; the biggest threats to the Drow species are its own culture and religion. What if the Order of the Spider represents a splinter sect that aims for stability and survival above all other things? They couldn't worship Lolth, then, even if its agents attend her services and give lip service to the faith.
Maybe they have a different, secret patron, or they're completely atheistic at heart. In either of these cases, they wouldn't be headed for the Demonweb Pits after death.

If she didn't worship Lolth Lolth would have killed her on the spot. ALL must worship Lolth, she does not share.

No necessarily. They may just temper their ardor, and be tasked by Loth to take a longer view of things. They may be "above the law" so that they are more immune to rampant politics of Drow society, or simply be Loth's "detectives" and so have greater latitude when performing this function. To date, we simply have not been shown very much about the order.

True but still, this is Lolth and not Ch'Thier so i doubt she would tolerate opposition even if it was in the end beneficial to her people.
Plus they are named order of the spider. Given that drow have no spidery features, the name has to connect to her somehow.

It might be a negative reference. The order's full name might be: 'The Secret Order Dedicated to Ensuring Drow Survival in Spite of the Spider'.

Maybe they are just the intelligence arm of the theocracy, sitting in the center of their information web and feeling the vibrations of its strands?
No more, and no less. Nothing in that precludes acknowledging Lolth as the ultimate ruler.