It means "from nothing". The word scratch is also used to mean : "the starting place, starting time, or status of a competitor in a handicap who has no allowance and no penalty.", which is probably where the "from scratch" phrase comes from.
English is not my first language so I'm not sure but scratch can mean that you write or draw something, so I thought it could mean that you are starting from the planning phase/drawing board, similar to the phrase "back to the drawing board".
Yes, "from nothing". It depends on the context, for example to make a piece of furniture, you might need to first go and find a tree, chop it down, prepare the timber ... and so on. But usually it might mean just use ordinary timber purchased from a supplier, but do everything to your own design and specifications, and so on.
I don't quite agree with the 'from nothing' definition.
There are two meanings that are similar:
1, From the beginning; starting with no advantage or prior preparation.
2, From basic materials or raw ingredients.