There are different types of multi output air pumps. I'm going to use pump mechanism to mean one diaphram setup and one vibratory pumping arm.
A TetraTec Deep water pump uses four pump mechanisms and two air outlets. Some pumps have two mechanisms and two outlets. So, the answer to your question about those dual outlet pumps is yes, they can have different outputs, but shouldn't as the parts are assembled pretty precisely these days.
Larger linear pumps quite often come with a manifold with several barbs for air lines, but use only one pump mechanism.