Yes, but if I am allied with everyone, and they are allied with everyone as well? If there are only 3 parties in the game left, and if A and B are allies, and I ally either of them, then that party I ally (say, A) will also immediately fulfill the conditions, because A is still an ally of B and now an ally of mine; we both fulfill the conditions simultaneously?

Here's the answer you're looking for.  If a=b and b=c, then a=c.

I have been noticing quite often that when I research alliances I do not have any option to create an alliance treaty with other sovereigns.  I do not mean that they do not accept the treaty but that the option does not show up for me to choose when I am proposing a treaty.

Has anyone else seen this?

I am wondering if the issue is that by the time I research alliances, some or most of the other factions have been destroyed (either by me or by another AI player)? Nevermind that once you have the ability to make these treaties it does not really matter if a faction or so has been destroyed...  Or is this just a bug??

Yes, when you win it's on the turn change.