I think you've missed the point slightly. This paper looks at two cases, one of which is the "two images, two embeddings, one operation" (eg siamese-style). They note that this works well. They then go on to note that the problem of "are these two components at aribtrary locations of an otherwise blank image the same or different" is not well solved. This cannot be addressed directly by Siamese nets (well, or at least kind-of-can't. Arguably relational networks are similar to taking pixel pairwise functions, and thus have some relation to Siamese nets.)

In any case, they directly exclude the case you mention.