I will try to keep this response brief.
1. Simplified English is not Human Factors and vice versa.
2. Simplified English was developed using linguistic structures, as you mention, to enable comprehension by those who do not speak English as their first language. In fact, I agree that Simple English must almost be learned as a separate language.
3. The manuals are not written for 'the average user'. The manuals must be used by all users, from the best to the worst. As such, they must be written in such a way that someone with even a poor command of the language and low level of competency can still understand them.
4. If your human factors training appears to be to assist you in overcoming your feelings of inadequacy from not having paid attention in the fourth grade, then either your organisation needs to change their human factors trainer or you need to listen more to the training presentations.
In summary, I agree that some of your examples could be better written. If it is the language that you object to, write to Boeing. They have a process for upgrading the manuals, based on comments from users. Also, you could try the organisation that 'runs' the language:
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