Many of the rules came about because a certain coach ran a certain type of offense, or had his players use a certain technique. Others can copy it but if anybody is more successful than others the rules changed.
The Notre Dame Box or Rockne Shift was a variation of Stag's Single Wing. It wasn't the first shift, Stag had one. The Minnesota coach before Rockne was a player would sometimes shift all 11 players like a "Chinese fire drill". Rockne's shift was much more effective in providing a supremacy of numbers at the point of attack and provided versatility putting all four backs into play. All four backs moved at the same time in unison overloading defenders ability to read and react.
Nobody in college football did it better than Notre Dame. The Green Bay Packers won several NFL titles running the Notre Dame Box. Other coaches complained lead by Fielding Yost of Michigan, a school that hadn't played ND in more than a decade.
It was banned by a rule requiring players to come to a full set before the snap. Then allowed one player to be in motion at the snap.
Somewhere back in those days there was an ND player who was very fast in any era of hook and laterals and similar razzed dazzle plays that resulted in frequent fumbles. One day in a game as other players dove for a loose ball on the ground, he kicked it ahead, outraced everyone to the ball and scored a TD. The coaches taught that "technique" to the other players. It was subsequently banned.
In the late 50's or early 60's one SEC defensive coach taught his players to tackle WRs, QBs, and slender RBs, upright. Stand them up impeding forward progress while other defenders would fly into the ball carrier with their heads lowered "spearing" the ball carriers body with their helmets. It caused lots of fumbles and spread throughout the SEC. It was eventually banned.
Around the same period one team came up to "tear away" jerseys. The strength of the fabric was purposefully weak so when a defender grabbed the ball carrier by the jersey it would tear away leaving the defender with a handful of material while the ball carrier broke away for a big gain. Some backs went through several jerseys a game. It was big in the SEC and SWC. Eventually the NCAA banned it.
Charlie Weis and Nick Saban spent an incredible amount of time on the road recruiting and were very successful with it. Other less successful head coaches who did not want to make the same time commitment, like Willingham, lobbied to get the rule changed to restrict head coaches time on the road recruiting.
Wasn't it just a few seasons ago that Bielemna used an unsportsmanlike like stalling tactic on defense? The rule was changed to stop his "innovative" technique.
Most of the rules were made because somebody had what others thought was an unfair advantage. So the others lobbied for a new rule.