I'm familiar with the Rolling Air Frame missile, and as you say, the physical damage to TWA 800 is consistent with the fragmentation warhead that the RAM carries, not to mention that it was a center-of-mass impact.
I have a hard time believing that the NAVY would not be using a remote testing range for something like this. This theory is one that I would be willing to look at since the physical evidence supports it.
A remote testing range has one serious flaw when it comes to this kind of weapon. If the weapon that is being tested is a missile that tracks a target's radio signature, then the ideal location of the test would be an area with a lot of random background radio "noise" -- in other words, a major metropolitan area.
Most people would probably be quite disturbed if they knew how many weapons tests are done off the coasts of major cities like Los Angeles, San Diego, New York, etc. -- tests that are done there precisely for this reason.