The narrator's father describes the Meseglise way as "comprising the finest view of a plain that he knew anywhere" (despite there being no visible horizon, but let that pass), and the Guermantes way as being typical of river scenery. These become, for the narrator, their defining qualities ("I had invested each of them..with that cohesion, that unity that belongs only to figments of the mind"). They become invested with a platonic ideal of a view of a plain or of river scenery where the abstract idea of them is more real than the actual ways themselves.
The two ways are separate and distinct in the narrator's mind, each unique and inviolate in their plaonic ideal isolation. Also, more prosaically. because the family only ever went one way or the other and only ever on separate days, never going both ways on the same day. This all serves to "shut them up. so to speak, far apart and unaware of each other's existence, in the sealed vessels - between which there could be no communication - of separate afternoons".
I have read this paragraph on the two ways about 50 times in the hope of gaining some insight. I am not sure it was worth the effort, in that all that Proust has told us is that there are two ways and he feels differently about them and thinks of them as separate, and one goes over a plain and the other down by the river. I think it is this sort of thing that puts people off reading him.
I shall press on anyway.