I could imagine for many carriers the shorter landing gear is a feature of the design; I believe some using this airframe choose to disembark passengers direct to the tarmac using the system's ladders, rather than involve a flight of stairs or an articulated gangway, lessening airport fees.
Edit: not to lessen any of the other points you made - this absolutely should have gone through approval as a new model.
The design predates broad availability of jetways at airports. The concept, in the 1960s, was that by being able to use stairs they'd be able to service many smaller airports. By the 1970s this was clearly the wrong choice -- smaller airports just installed jetways too. This was a design decision that didn't even last the decade, but was brought forward for the next 50 years because changes would mean a recertification. That is why the landing gear is short. There are essentially no operators who make use of the low height of the aircraft, and there hasn't been for longer than most of us have been alive.
Edit: not to lessen any of the other points you made - this absolutely should have gone through approval as a new model.