I'm drawing the map like this:

-- 2 is the layers count
for i=2,1,-1 do
   map(fetch"map/0.map"[i].bmp)
end

And I can check for collisions for map tiles with fget(mget(x/16,y/16)) to get the flag of the tile, all good here, except I can only check for collisions on the top layer, while every other layer is ignored.

How can I check for the flags on every layer?

Try: get(fetch"map/0.map"[LAYER].bmp,X_POS,YPOS)

is get a function or do you mean fget?

@merwok No, I meant get. get is a function for looking inside userdata, which is necessary because mget cannot look at anything other than the top layer, so a call to get with fetch"map/0.map"[LAYER].bmp as the first argument is being used instead of mget.

Thank you, that works perfectly, this opens so many options now.
I could do collisions only on a specific layer, or all the layers!

I think I'm going to dedicate a specific layer to being solid and have a background and a foreground layer exclusively for decorations, I suppose I could even dedicate a layer to object markers, the layer would not be rendered but a function would scan the map and spawn the corresponding object on map load.

Here's some code resulting from my tinkering:

Layers definition:

LAYERS = {
{index=4, name="background", render=true, render_objects=false, spawn_objects=false},
{index=3, name="solid", render=true, render_objects=false, spawn_objects=false},
{index=2, name="foreground", render=true, render_objects=true, spawn_objects=false},
{index=1, name="objects", render=false, render_objects=false, spawn_objects=true}
}

Note that the layers must be specified backwards if looping forwards

Drawing:

function _draw()
	cls(0)	
	foreach(LAYERS, render_layer)
end

function render_layer(layer)
	if (layer.render) then
		map(fetch"map/0.map"[layer.index].bmp)
	end

	if (layer.render_objects) then
		-- Render all objects here, in this case my player is in a table but anything can be rendered here
		for p in all(player) do
			p:draw()
		end
	end	

end

And finally, my collision functions:

function get_layer_tile(x,y,layer)
	return get(fetch"map/0.map"[layer].bmp,x,y)
end

function is_tile(tile_type,x,y)
	local tile = get_layer_tile(x/tile_width,y/tile_height,3) --Hardcoded to solid layer, which is 3
	local has_flag = fget(tile,tile_type)
	return has_flag
end

function is_tile_solid(x,y)
	return is_tile(1,x,y) == 1
end

At this point there's really no more need to actually check the flag of the sprite, but it can be useful for advanced behavior