"* Player A is on second base. Player B doubles and drives him in. Player A is credited with +1 (run), while Player B is credited with +1 (RBI). That is two points created in your system for one run."
Not it isn't. If you were looking at it in terms of a team then yes, but he brought it down to individual players. The idea is looking at an individual player and saying if he contributed to scoring a run, both of those players contributed to scoring 1 run. Which if you look at it, the formula would say. Now if a player hits a homerun, if you keep homeruns then you saying he contributed to 2 runs scored which isn't the case.
for the record, I'm not saying if this is a good or bad way to judge a player, just explaining the logic of not using homeruns which if you were to do a formula like this, I would agree. Although I will say it isn't the best form of evaluation