Well what do you know, I found a shot of my desk I had taken with the stock app to check for aliasing on hard lines.
I tried to line up a similar shot with my phone now that I've flashed the zip to reduce sharpening and NR, but the mess on my desk is somewhat different now, so it doesn't line up exactly. Also, the newer shot picked a different exposure so it seems more evenly lit, however I don't think that has anything to do with the modification. That's just me being more careful with setting the focus / exposure point this time around.
But you can see the 2nd image doesn't suffer from the over-sharpening thing, and the fine detail in things like lines and letter is preserved. I have no idea why Moto decided it was better with all that extra stuff on, this is clearly nicer looking to me.