If they're declared *At War* straight from the setting phase, the "prefs.ini" file will list these two race slots as having such relation status permanently -- UNLESS, another game modifies both the ID numbers and their corresponding status.

I figured this out while i was developping X-Worlds as i wanted to maintain some friendly or other status between the Humanity races or_and their 'natural' enemies - any of the Aliens.

Example; The Interceptors needed to be Close enough to the Magnetic as to be very near Alliance (once the tech is shared by them & activity provided the opportunity for the player to offer it to an AI... given a game has initialized them to play with, btw) BUT, both also had to be AT War against the Sectoids --- from first game starting turn.

Once, you quit or save such games, the configuration files **presume** the relation status between race slots is somehow 'static'. If the opponents structure and choices remain as is.

@Scoutdog: You, as the player, can gain either "Historic Friendship" if you maintain friendly relations with another race for I believe 5 game years (it could be 3, which I understand is a big difference, but its been a while so...)

If you declare war on another race, make peace, and come back and declare war again, eventually, your reputation/credibility will be so damaged that you will have "Historic Animosity"

The Torian and Iconians have this toward the Drengin and Yor respectively

Edit: As for modding: It can't be done.  The Diplomatic relations (what causes the various + or -) are hardcoded. You can set their overall attitude, but thats it. Sorry.

In what it probably my single most idiotic mistake ever, I got the name of what I was looking for completyely wrong. It is actually called "lingering racial grudge" not "historic animosity."  

Through some experiments and liberal use of cheats, I figured it out: The race that has raceID: 4 in the raceconfig.xml will always have a problem with the race that has raceID: 1, and raceID: 5 will never get along very well with raceID: 9. They will have a permanent diplo penalty called "lingering racial grudge" when dealing with each other, like the Torians and Drengin or Iconians/Yor.