People often underestimate the adaptability and plasticity of their own brains.

Your eye can "adapt" to widely varying images and integrate it into a usable image--this is why many people are able to comfortably use uncollimated binoculars, vastly differing (or even different phosphor) tubes, etc. In many cases, some people may have a slight difference in the visual acuity of their individual eyes--this is mostly noticed when you're getting corrective lenses (your two eyes usually require different prescriptions), but it can be present even if folks without corrective lenses if neither eye is "bad enough" so as to warrant eyeglasses.

That being said, the more different the images, the harder your brain has to work to integrate that image, which can lead to increased long-term fatigue, which may or may not lead to headaches or other physical symptoms. However, as is well known, fatigue can also have mental effects that affect situational awareness, decision-making, etc. However, from a person-to-person standpoint, using goggles briefly in a more recreational context, a person might not immediately notice or recognize these affects.

To the original question, do differences in resolution matter in a binocular system:

Depends on whom you ask--most users probably will not notice the difference assuming other specs are similar.  

According to the manufacturers, matched FOM is more important than individually matched specs and per NVESD / RTI there is still a direct correlation between overall FOM and Detection / Range / Identification (DRI).

Aviators in particular are extremely interested in resolution, with the most common reasoning being given for seeing wires--greater resolution allowing an aviator to see a wire even a fraction of a second earlier is still considered an extremely important factor.

~Augee