I don't disagree with everything but your last paragraph.
With that said, if Shanahan plays more conservative on offense and didn't ask his rookie QB with one start to complete 5 different 4th down conversions, including 3 while they were in FG range, the game is likely much different. If you want to talk about only the 4th down plays, either Shanahan made poor coaching decisions, or Kliff/Vance outcoached Shanahan on the plays themselves.
Let's break it down a bit smaller. Has there ever been a coach that has outcoached the opponent and lost? IMO the game doesn't have to be a blow out to be out-coached.