The Freight Train that appeared in the magazine was almost completely scratchbuilt, except for a handful of kit parts. Plus, it was not based on an existing kit. Is it absolutely 100% scratchbuilt? No, technically not. But about 95% of it was, and since it was not a modified kit, I think it deserves the "scratchbuilt" title.
The modified in this thread began life as a kit. Yes, it's heavily modified, but still began as a kit. I think that's the difference here.
Yes, this topic can easily fall into the "splitting hairs" category.
Just how much of a model has to be truly scratchbuilt to qualify as a "scratchbuilt" model? That depends on who you ask. But a model that begins as a kit, and is then modified, added to, and includes scratchbuilt components, can't really be considered scratchbuilt, IMO. "Scratchbashed," maybe.
Gerald Wingrove builds truly scratchbuilt models. He starts with drawings and a pile of raw material... and he literally creates every piece of his models using those raw materials. "From scratch," as it were. No existing kit parts are used. Zero. His models are truly scratchbuilt, and the best example of the meaning of a "scratchbuilt" model.