I don't get what you are trying to say though. If companies can use 'a mile long paper trail', why can't the engineer do the same?. If it turns out they were forced to do X over their own objections (people do have mortgages and need medical coverage), then that manager gets the blame. Seems fair??

CYA emails are not exactly a new concept. Perfectly acceptable from rank and file engineers. And the more senior people you are sending that to - if they are not clueless which does happen - know exactly what this is about.

Project documentation also not a new concept. Also acceptable.