Actually decapping the original chips is very much a thing. See for example Chris Smith's work mapping out the innards of the ZX Spectrum ULA - http://www.zxdesign.info/book/insideULA.shtml .
Theoretically it would be possible to automate this with a couple things:
- USB electron microscope to image the transistor topology
- CV lib to identify connections and generate corresponding Verilog code
My understanding is that there are people who do it often enough that it is automated in the way you describe, but you still need someone with a lot of skill to spend serious time on it. Computer vision works wonders but there are errors which must be identified and fixed.
A lot of the chips people care about are can just be done optically, no electron microscope needed.