I was watching a gameplay video the other day and they mentioned that the 3DS version doesn't have jumping, so hidden items are reached in different ways, e.g. by walking across ropes. So between the 3DS and PS4 versions, the map layouts are probably quite different.
That said, the 2D and 3D versions on 3DS already have somewhat different map layouts, and you can only switch between them at a church. From the little I've seen, I'd guess that it probably would also be possible to mix and match the 2D and PS4 versions too if they really wanted to.
(Perhaps there are other gameplay systems that differ between the two, though?)
That would make sense, cause, as charming as can be the 3ds version, i really think it would be a baaaaad message to send that Switch can only afford the 3ds remaster of the game.