Pat,
I think these alterations usually have more political motivation than architectural motivation.
Oak Hill is an example that is very close to me, and it is one that I have never quite understood fully. One of the reasons Oak Hill made some changes was that holes 5, 6, 15, and 18 all seemed too congested during tournaments. The old 15th green was bordered immediately by out of bounds, and the 18th green was thought to be too close to the clubhouse. So, the club brought in the Fazios to make these holes easier for the crowds.
That was the standard explanation. However, the Oak Hill members' issues with the course seemed to go beyond "congestion." There seems to have been an issue with the outcome of the 1968 US Open. Lee Trevino won the Open as a Mexican-American who became the first player to break 70 in all four rounds of a US Open. These two facts seemed to irk the members, and they wanted to make the course tougher to prevent such an outcome in the future. While there were some structural issues with the course's ability to handle major championships, politics played a major part in the changes. As a result, the Fazios came in and desecrated some of the best holes on the course.
Interestingly, the course was easier in 1980. Jack Nicklaus (one of two players to break par in 1968) finished one better than Trevino did in 1968 and five better than his own score in 1968. He won by seven shots.
Of course, Oak Hill had been changed well before the Fazios entered the picture. Robert Trent Jones completely altered the course prior to the 1956 US Open. I'm not sure of the full extent of his work, but he rebunkered every fairway and green and changed several green complexes. In the case of both the Fazio and Trent Jones renovations, the work was intended to make a seemingly insufficient course tough enough for championship play. In reality, the work was done at Oak Hill to pad the egos of the members in charge.