OK, maybe a compromise. As it is you can only work on the chambers you can reach. This is very inefficient, especially if you have multiple passageways to work on. Making the small amount of units needed is just inefficient and if you make in bulk most dragons have no place to store this (mainly because the storage system in use doesn't account for the new crafting requirements...multi-resource items).

So thinking along the other construction involved in this world why not make it so that players can only apply construction units to chambers on the same level. That way when I makeflawed flowstones in bulk Ican apply them to all passageways on that level.

What about multi-layer structures? Well that can be done in one of 2 ways. Either you can apply to it because its on the same level or you can't. Thats the compromise.