I have mixed thoughts on this, and I think it's less hard to prove/logically deduce then some people make it out to be.
First of all to get this out of the way, Ashley Poprik was not the lead writer; she was an intern writer. Second, James Stevenson denied that the facial scan actress changed, and Poprik denied being the facial scan model outright.
What they fail to mention is that facial scans are then edited, obviously to be fair. Modelers have to adjust topography, proportions, fit the rig, etc.
So my theory has always been, someone said MJ looks too sexy, and that they need to make her look more like an "average" redhead ("not an ugly girl, just one you could meet on the street!"). So where do you find an "average" redhead who you can use as a reference and who has literally zero legal standing to sue whatsoever? Easy, your own team. Most AAA developers include a boilerplate likeness release (usually for Behind the Scenes footage and what not), so image references are on the table as far as I know. Poprik wouldn't even need to be informed that she was a reference unless it was a true 1:1 recreation, which it isn't.
It's never been explicitly confirmed that that's the workflow, but I imagine it's probable and won't be confirmed ever, period. It is confirmed ND did something similar with Abby from TLoU2, where she's an amalgam of two different women (three if you count the VA), which is why she looks fucking weird.