Both of the references are taken from NCAA 2002 rule book:

7-2-d . For the purpose of determining when a player or players may be released from a penalty, for all time--serving penalties called on players of opposing teams from the time the flag is dropped or the whistle sounds stopping play (whichever occurs first), until the sounding of the whistle resuming play, the lesser amount of penalty time shall be treated as non-releasable.
When two or more players from opposing teams are sent out of the game, and the penalty time for each player is the same, the players shall not be released from the special substitution area until their full penalty time has been served.
If the penalty time of a player(s) on one team is longer than the penalty time of a player(s) on the other team, then no one shall be released from the special substitution area until the shorter penalty time has elapsed. At that time, the player(s) with the shorter penalty time shall be released from the special substitution area; but the other player(s) shall remain until such time as his penalty time has elapsed, or his team has been scored upon.

A.R. 4. A1 has possession of the ball. B1 commits a technical foul. On way to special substitution area, B1 is assessed an additional one-minute personal foul for maligning the official. During the first minute of B1’s 1 1 /2 -minute penalty, A1 scores a goal.
R U L I N G : B1 must serve the full one minute of non-releasable time. The penalty is releasable for the final 30 seconds.

Hear is the question: In 7-2-d in the rule implies that any goals that accrue in the shorter time have no effect on the releasing of the longer time. This is obviously different than the A.R. I also posted. Is this a special exception during simultaneous fouls or am I reading way too much into this?

Your quoting of rule 7-2-d applies to simultaneous fouls...fouls that occur on both teams.

I believe the situation you cite at the end of the posting has only the B team accruing penalty time. That is not a simultaneous foul situation because the A team is not serving penalty time as well.

Now...that may not be your question (I am a bit confused by your question). If B is in for two fouls..one non-release (which must be served first) and one releasable (served second)...then A can score and score and score during B's first minute and he stays in the penalty area. Once that first minute is up...then he starts with a "clean slate" for his second penalty..i.e. if A now scores...then he is released. (In other words, all those scores happening during the non-releasable minute have no bearing on that releasable time to follow).