basically, the platforms/tracks issue was one they should have tackled when they built this MSG back in the 60's
Not the city's call. The station, the tracks, and the tunnels under the river were owned (at that time) by the Pennsylvania Railroad. (They are now owned by Amtrak.) They were privately financed and built in the 1900's. After the WW2, breakthroughs in air travel began siphoning off long distance passenger traffic from all railroads. The federal highway act began siphoning off medium distance traffic.
Greyhound buses could operate at a far less cost, because they used government built roads. Railroads needed to maintain their rights of way, not to mention pay taxes on them. Airlines paid fees to municipalities to land and take off at airports. Every limb was being cut off the railroads. By the middle of the 50's, the most profitable thing railroads could do was move freight long distances. Penn Station NY didn't have a role.
If you see photos of old Penn Station towards the end of its life, you will see that it was not maintained. It was dirty, filled with soot, just like Grand Central before they cleaned it up. It looked like a dark, grey, soot filled tomb. People wanted new. And new meant jet travel and auto travel. People stopped using trains for long distance travel.
In the 60's everyone assumed the train was going to go the way of the horse buggy. Gee, cars can't move the 10 million people living outside NYC easily in and out? You don't say!!
Actually the LIRR was filling the coffers and was one of the most profitable arms of the Pennsy. The success of the LIRR turned Penn Station into a commuter RR depot; it was no longer the long distance depot it was designed to be. PRR no longer needed all the red-caps, all the ticketing offices, all the baggage handling areas. They were losing money hand over fist on Penn Station, and were very eager to get rid of it. (They were losing $1 million or more a year in operations on the station back in the 50's. The PRR did to Penn Station what the City of New York did to the old Miller Highway on the West Side - as little as possible to keep it standing.) When the Garden came calling looking for a new home, the Pennsy was more than happy to divest itself of the structure above the street. They got their smaller station, suited for the operating conditions of the time.
Remember, no tracks or platforms were removed during the 60's. The amount of walking space (square footage) found in Penn Station for passenger movements now is comparable to that in 1955. The only difference is when you look up. In 1955, you looked up and either saw an iron and glass train shed or a huge waiting room with murals of world maps. Now, you look up and see fluorescent lighting fixtures. The concourses were ALWAYS below street level. The Main Waiting Room was below street level. Even the taxi-ways were below street level in the original Penn. The only thing at grade was the arcade of shops on the 7th avenue end, which is now the atrium area around the office tower and the entrance from 7th avenue to the Garden.