Google didn't pay that money just to bypass the formalities along the way to paying a fixed fine - they paid it in order to head off the possibility that they were going to face a jury trial instead of a bench trial, since juries are far more likely to vote in favor of much bigger fines than judges are.
Sounds a bit unusual, but not unfair - Google just preemptively paid all of the damages that the government was seeking in this particular case, which is the only thing the jury would have been needed to determine. So having a jury would be a complete waste of the jury's time. The rest of the case would be up to the judge anyway.
If the prosecutor thinks they could get more now maybe they should have asked for more earlier. I think this may have been a miscalculation on the prosecution's side.
The nice thing about trials of corporations is discovery. We have evidence of Google intentionally making search worse, increasing the time spent looking for results, and this improving ad sales. All that came out in discovery.