In the hierarchy of "from scratch", it goes more like "buy fast car", "build fast car from available parts", "machine own parts from stock", "make own castings from scrap metal", "mine ore and smelt it".
Just because my hot rod isn't made from existing parts does it mean I'm mining ore.
Many awesome hot rod projects involve machining from stock or even casting from scrap. What OP is doing is on this same level. He's not doing atomic layer deposition or anything. Just writing code on top of an existing OS and using existing programming languages.
If you want to make something custom you don't need to start from scratch.