First, note that the Meriam Webster definition of see, #2 does not say, "become aware of something by using something other than eyes". It's just "become aware of something"; it doesn't matter if the eyes are used or not.
The confusion is that the act of seeing is often intrinsically linked with acquiring knowledge. Often, knowledge is acquired through vision. But then how could one ever decide to use Definition #2 if Definition #1 always seems applicable?
The key is that a definition #1 is indicated when vision is the focus of the meaning, primarily assumed, or required. Definition #2 is indicated when the focus is awareness or knowledge rather than vision. Here's a general test one could use to determine whether or not the "visual sense" or the "knowledge sense" should be interpreted:
- Would the statement still have the same meaning if some people may have gained the awareness/knowledge through means other than direct vision?
If no, then the emphasis is on the visual sense, and favor Definition #1.
If yes, then strongly consider the "awareness/knowledge" definition since vision is not required.
Now consider these sentences:
- We have seen his work. He's very skillful with watercolors.
In this case, the speaker is talking about an actual instance of vision since, presumably, one typically requires vision for seeing visual arts. Now consider the target sentence:
- We have seen better test scores than this.
While vision might have been the method for acquiring the prior knowledge, that is not a requirement. For some people, the knowledge could have been acquired from a lecture or a meeting. And most importantly, the teacher's main message is not about a prior act of seeing something with eyes. The teacher is comparing a prior fact with a current fact. It is the knowledge of the test scores that is being emphasized, not the visual sensation. Definition #2 prevails: to have become aware or to have gained knowledge.