This has been my thoughts as well. So many things that lead to a conspiracy theory forming can easily just be poor management, planning, etc.
I think Kennedy and his handlers pushed no bubble top and not agents on the back bumper due to the optics. He was in Texas mending fences leading up to the re-election run.
A similar scenario these days could have the Presidents handlers pushing for these things and the SS pointing out that they are not budging, then reminded them that JFK is the reason they are not budging.
Short of Hinkley they haven’t had a gap since. Part of that is luck. But a big part of that is they greatly ramped security and won’t budge on it for any of the reasons they allowed themselves to be budged on on this day.
but you'd think if they allowed open air car with no agents on or even really that close to the car that they'd have a better sight and control of surrounding buildings.