In terms of bonus fleet ship types, starships, guard posts, guardians, fortresses, and things of that nature: yes, you'd encounter all of that eventually.
In terms of the specialized buildings like alarm posts, counter-spies, and so on: you'd encounter most of them in a really rare sort of fashion, but I don't think quite all of them. There's a very low percentage chance for you to encounter a lot of that sort of thing with any AI type, but that tends to wind up playing pretty different from encountering them en-masse, for instance.
In terms of some of the really specialized behaviors of the AIs, some of which involve special ships, you'll never see any of them without playing with their relevant AIs. For example:
- Without playing against a speed racer, you'll never see an AI with all-fast stuff like that.
- Without playing against an experimentalist, there is no other way for the AI to get experimental ships.
- Without playing against a support corps AI, there is no way for it to use those sort of ships in any significant volume.
- You will see special forces guard posts obviously without playing against a special forces captain, but having them in such high volume really changes things around.
And there are many other examples of behaviors or overall "feels" that are accessible in any other way other than playing with that AI type.
In terms of the minor factions, AI plots, etc: the only way to encounter any of them is by turning them on, but you can turn them on with a vanilla AI just as easily as with any other sort of AI.