I believe that in this case, IndianaUmpRef makes a call based on 2 facts:
1) Defense obtains an unfair advantage by positioning F3 in a manner to block the bag. Previous instances were significant enough to warrant a verbal warning to the offense (In his opinion - remember this is a judgement call)
2) F3s actions place him in a position to cause injury to himself and possibly R1. This risk is assumed by IndianaUmpRef to be more profound than the normal course of the game.
In FED, we constantly emphasize 2 things, safety and sportsmanship. I think that IndianaUmpRef makes a valid case for this instance being at a minimum a questionable play and therefore could result in a judgement call be the umpire, in the interest of the 2 FED "talking points" - safety and sportsmanship. He attempted to rectify the situation with out a penalty, to no availe. Thus, a penalty is justified.
As umpires, especially in FED games, we are forced into bugger picking in the interest of safety and/or sportsmanship. Often, this can result in an earful from the coach/parents, but aren't we on the field for the kids?
IndianaUmpRef, from the info you provided, I think you made the right call, considering the circumstances and your previous warning. However, in the future, I would make sure that this play is not similiar to a catcher positioning himself to make a play at home.