My theory is this: Seth is an alternative name for Sithis.
Firstly, the Brotherhood of Seth is an actual thelemic body, documented in the early 80's, membership is still available. This website has a good overview of beliefs et cetera, as well as documentation from the original members: http://www.holycovenant.com/index.php?id=10" onclick="window.open(this.href);return false;. There was also a group named the Knights of Seth who attempted to resurrect dualistic Christian ideals around the 1850's. I don't think the Bethesda Brotherhood of Seth has anything to do with these groups, I simply thought I should include the information, also there are lots of symbols used which we could use for motifs/sigils within High Rock.
However, as discussed the name Seth can be seen in many different religions, the most notable is the Egyptian God of Storms, Set (which translates to Seth). He is the God of storms, confusion, chaos et cetara and generally regarded as a real knob, very similar to Sithis, in Elder Scrolls lore.
Secondly, the entry text displayed to the player upon arriving in the city of Gideon in Black Marsh in TESI: Arena, reads as follows:
This indicates that the followers of Seth have an area of influence in the city of Gideon, Black Marsh. I think this is important as The Argonians have a particularly strong tie to Sithis, most notably in the form of Shadowscales. It has also been stated that the sentient Hist tress of Black Marsh, are aware of the presence of Sithis (The Monomyth), again indicating the influence of Sithis in Black Marsh.Gideon, the black city of the followers of Seth, lies near the southern tip of the Imperial Run. A cold air that has nothing to do with the time of year seems to chill your bones as you enter. It has been rumored that the Shadowblades, who fight for Gideon, are undead...
Continuing the connection with Argonians, Camlorn, where the only plot related Temple Of Seth is located, is a coastal town; the Argonians affinity for water is well documented.
Thirdly, I do not think it seems too far fetched for Sithis to have an alternative name. Both in real life, and Elder Scrolls lore, deities have numerous titles. It seems likely that Sithis, the representation of chaos, may have many names. Sithis is also connected with both the Morag Tong, and the Dark Brotherhood, silent and secretive organisations focusing on assassinations, it makes sense to use an alternative name so suspicions are not aroused.
Obviously this is simply speculation, however I think interpreting Seth as Sithis, could provide some very interesting plot points/quests et cetara revolving around both the Brotherhood, and the Crypt Of Hearts.
The only other interpretation of Seth I could find was this from a discussion on the UESP:
Any ideas/comments/criticisms are much appreciated!If the lore on the deity known as "Sep", a snake deity, is examined, can a connection be posited between these two - i.e., is "Sep" another name for "Seth" and vice versa. Again, the connection is based on verbal similarity and the physical natures of snakes an lizards (and by extension the Argonians). They share much in common: cold blood, scaled hides, carnivorous diet and so forth.