Basically, this is how I think it works:
1. Total number of altars: N = 3 (default), Crusader: N+1, Conjunction Prep: N+1
2. Select N random altars from the available 9.
3. Order of the N selected altars: Random
4. Player preps C number of altars (excluding Conjunction).
5. Player gets the C number of altars that are prepped.
6. Remaining (N - C) altars are taken from the list (after Step 3) starting from the first in the list and so on, skipping over those that the player have already prepped.
So far, based on the results of the previous dailies, the order of the selected altars is not alphabetical and it does not follow a fixed order ("last 2" dailies with test results put 2 gods in "opposite order"). So, it has to be Random.