You're not missing anything. Pre and post 485 application are two different things.
Pre 485 application your only status is h-1b. Therefore, you have to ensure that you didn't violate that status (I haven't seen one issue/posting where people got paid less and it has been an issue for them. It has been an issue for the companies if you sued them for pay).
Once you apply for 485 then your main status becomes the 485. If you work after the application is filed then you have to have EAD or h-1b. Once again low wages would not get you in trouble but the company.
The main way you get in trouble is if you worked for another beneficiary or in another location that wasn't allowed by h-1b.
For arguments sake, let's say I'm an adjudicator and I have to abide by the law:
From the biographical information I would see all the places you last worked for the prior five years when you submitted 485. I would look to see that the locations and companies you worked for would be allowed by h-1b.
I would then look to see when you entered the country and if there were any gaps in h-1b (ie., transferring between employers without filing transfer of h-1b).
Since the adjudicator doesn't know what you did biographically after the 485 has been submitted they can then request w2's paystubs to determine after the 485 was filed did you engage in any unauthorized work. If you had EAD then none of the work would be unauthorized.
I agree that having low wages prior to 485 being filed can raise questions; such as were you working or were you just using h-1b to live in the country and you had been laid off, etc. I think you have stated that you have good justification for this.
However, keep in mind that pre and post 485 the situation is different. After 485 is filed that becomes your status to stay in the country and you don't have to do anything as long as you can show you have a job lined up upon greencard approval that meets the labor certification requirement.