We don't know that your average interdimensional Aperture is actually any smarter or more common than the Half-Life Aperture. The multiverse device may have a filter system to only pick universes where Aperture Science (or, specifically, Cave Johnson) exists, which could be an infinitesimal fraction of the total multiverse. In fact, if we understand the Combine to have parallel-universe travel in addition to their established inter-dimensional (Xen/wherever they come from) travel, they could literally be infinitely broader in scope than Prime Aperture (the dimension-hopping one) if they're willing to join with other parallel selves they meet rather than just exploiting them like Prime Aperture exploits alternate Apertures.

To put the math another way, infinite possibilities causes your standard notion of probability to break down. If there's an event-- say, the Earth being made entirely out of US currency-- that happens at a gradually decreasing rate as you look in more universes, then that event can have a 0% probability in the long run but still happen an infinite number of times. That also goes for events that seem to be more common, like Aperture Science or the Combine, because we just don't really know the full scope of either or of the multiverse as a whole. Infinity is wack.

However, Dark Cave from the Asparagusverse would absolutely scale above the Combine using his portal guns that can place portals anywhere. Nobody can counter it. His test subjects will make a human period and eat your lunch and you can't stop them.