Well, the in-universe logic is that the AI just doesn't care enough about you to bother. It's the same story-reason it doesn't immediately send every unit on the map at you the moment you start the game. On the other hand, during the Showdown, you're actually threatening the AI in our galaxy, so you get some extra "special" attention.
More practically, players don't like the counter waves, so they are very limited in use. Counter-attack guardposts, Warp Relays, and the Showdown - all of which can be turned off. Even the Warp Jumper AI type can be easily avoided, along with the Backdoor Hacker (another unpopular AI type). In earlier versions of the game, Counter-attack guardposts were common, and you'd be a lot more familiar with the mechanic (whether you wanted to be or not) before you could begin a Showdown.
And the AI doesn't actually follow the same rules as the player. It doesn't manufacture units, have resources, perform research, or anything the player does. Almost all of the AI mechanics are different, so this continues the trend.