By your logic here, what is the use of having any resource cost at all? It is just unnecessary grinding for stone and wood, as you say. We are talking about survival mode, this implies some level of realism. Buildings need resources, and those resources require effort to gather, and larger structures should need more resources than smaller structures. In my opinion the ability to build a large simple but effective roof using 1 single unit of stone or lumber damages immersion in a survival game. All I am suggesting is that we scale things to resemble the current java balance of resources vs construction element size, it wont be any more grindy than the java game in its current state.
We already have creative mode for people who want to remove the grind of resource gathering and get straight down to building. The entire nature of survival games is to introduce some time consuming elements to achieving your goals.
I think it is fine to have a minimum cost of 1 stone even for smaller blocks, we don't need to be dealing with fractions of resources. Just round every calculation up to the nearest integer value, problem solved.
That is no logic from your side 
I am not against costs. Just increasing costs sounds to me unnecessary. Yes, its realistic but where is the point?
The situations where you can use a huge block (in whatever shape) are rare. If you build a giant wall and scale up the parts you should see it in relation to the wall. There even a huge block will be just a tiny brick in the wall.
If you build a wall for a normal house with just one block you take yourself the possibility of adding a door or window. Of course not all houses have windows or doors on all sides but on most of them. And most players here in this game are looking for details. so they usually won´t take this approach and prefer to build that wall with several blocks.
The roof is a good example from your side though and a valid point. Its also one of these rare occassions where you can really create a big area with just a few blocks. However is that rare occassion really worth the effort?
We are not even having a finished building aspect. I am sure (or i hope so at least) some type of material will need to be processed before you gain it in the future. i.e. roof tiles might need wood instead of stone and that wood needs some work first. Or tiles made from clay might need to get burned in the fire first.
As i see it raising the building costs would be a more realistic approach but add nothing to this game specifically. Instead i would suggest to raise the efforts to get a block at all. Several mineral types, processing possibilities (i.e. the above mentioned burning-part for roof tiles or pottery) and also several types of material (stone and wood but maybe also hay from dried grass, gravel, etc).
Additionally some tools that have to be crafted before some shapes or textures are available would be nice.
Raising the costs individually for each block when its placed sounds like a extremely difficult task to me. You already crafted a block and that block has certain capabilities. Im not sure if it would be as easy as you imagine for the game to calculate how many additional ressources or blocks you need when placing it.
