Yes, everyone agrees that they were refering to IMAX. It is also legal for them to do so (and for Ars to publish this opinion) without seeking permission from IMAX first. Some people on HN are surprisingly disagreeing with this (or at least condoning IMAX's response)
Also, the law shouldn't be that trivial uses of the mark like this work to erode it, but the law is not precise on the issue so mark holders tend to have to be verzealous in showing their defense of the mark.
This letter is just a lett-er not worth the non-paper it's not-written on.
The whole purpose of the letter is to be able to show diligence in court if the mark is threatened... not to attempt to get Ars to do anything different.
Are should know that too... but I guess they feel this is good link bait. (personally I think it adds tarnish to Ars's reputation, by making them look like rubes.)
No, this is absolute bunk. There is no reason for this. At least in the US this is protected by Nominative Use, which guarantees that "a person may use the trademark of another as a reference to describe the other product, or to compare it to their own."
Further: "Nominative use does not require that ownership of the trademark be acknowledged, for example by use of a sentence such as "UNIX is a registered trademark of The Open Group"."