When it comes to the chips, here is what I think (it has been suggested, but never actually spelled out) ...
As we know, there are 4 Apollyons that are currently accessible ... NW and SW accessible from the Swirling Vortex to the west (from the Dem Telepoint), and NE and SE, accessible from the Swirling Vortex to the east (from the Mea Telepoint). Each of these drops a different chip upon completion.
If you touch the entrance to either Apollyon (where you actually enter the battlefield) without the appropriate key item, it says "There are several six-sided indentations and a thin slot in the center of the circular dais here." which seems to be a clear reference to the chips, and the key item as well (when you enter Apollyon, it references the red (or whatever) chip being inserted in to the thin slot).
Now, we have NE, NW, SE, and SW; however, the dialog tables also make reference to one more area: Central Apollyon.
In my opinion, what probably happens, is that if you have the key item, and trade all 4 chips from the Apollyon areas to the entrance, your alliance will be given access to Central Apollyon, which would be considerably tougher than the normal Apollyons, and would have a mega-boss battle at the end (I think that SOMEONE reported seeing "Proto-Ultima" and "Proto-Omega" in the dat files for Apollyon and Temenos respectively, but I can't confirm this ... however, they would make sense as the ultimate end-bosses, especially given the presence of these ultima and omega parts).
I imagine the same thing applies for Temenos as it does for Apollyon with a special Temenos area at the end; however, I'm too lazy to find the dialog tables and mob information for Temenos.
Edit: I found Temenos string tables (ok, it wasn't that hard ... it was the previous dat file :wink
... and they are pretty much the same way. In addition to the West, North, and East Towers, there are references to Central Temenos