The term from scratch comes from starting from a position of not having a competitive advantage, like a handicap in golf or a thirty-second head start in a race. It was used in the 19th century when describing sporting events. For runners, some folks contend that the starting line scratched in the dirt was the origin of the phrase.
From a cooking perspective, it means that the chef is making everything from a position of not using pre-made or purchased convenience items. If she is baking an apple pie, she is not buying cans of apple filling and dumping it into a frozen pie crust. She's take the time to get the apples, slice them up, sugar them down, and put together a homemade crust from simple ingredients.
If she is making Pad Thai, she's not going to the grocery store to buy a pre-assembled box of spices and noodles, adding water, and then claiming she made it all. She'd take her time and put together the individual ingredients herself, adding in her unique take on taste, and spending the time cooking it to perfection.
While it may be convenient to have the ingredients pre-measured in a colorful cardboard box, sometimes it just tastes better to make things from ingredients of your own choosing. I'd take a Momma-burger or French toast over frozen stuff one pops in a microwave or toaster before consuming.
Slightly off-topic: It's funny how folks think about women as being cooks in the kitchen whilst not lumping them in with professional chefs. A chef is someone who knows how to make things with unique twists off of the usual recipe. Never did see any gender requirements in the moniker.
Iron Noder 2017