1. "...the Long Island Commuter Railroad (LIRR) in New York City, which has no freight traffic" - Incorrect. The LIRR also is host to the New York & Atlantic railway, a freight line which does indeed operate on LIRR lines daily. Average train gross weight is about 1,200 tons for each freight on that line, not 100 tons.
2. "FRA staffers point out that it is unfair to compare US buffering standards with those in Europe because passenger rail in the US has to contend with more (and heavier) freight traffic." - They are quite right to do so. The US plays host to the highest density of freight rail traffic in the world with most trains exceeding 5,000 tons (some closer to 15,000).
3. "In both Europe and Japan, a competitive business exists in the DMU marketplace. But that market is off limits to US transit agencies because the FRA has effectively created a trade embargo." - Incorrect. In San Diego, the Sprinter lines use Siemens Desiro DMU's, a light design totally unadapted for the US Rail network as far as weight goes. The line also plays host to freight trains at night. How they got around the weight requirement, I do not know. Furthermore, the San Diego Trolley has the line from downtown to El Cajon by way of Lemon Grove. That line also plays host to freight at night - a streetcar line! The market is indeed open, but the trick agencies use to get around the requirement is a bigger question.
4. "The FRA proposed rule would only allow Quiet Zones exemptions at crossings that had been improved with "four-quadrant" gates and curb medians." - for good reason! Many fatalities happen at grade crossings and horns are one of the only really efficient ways to keep people off the tracks. Most other nations have few crossings, preferring grade-separated rights-of-way. However, in the US, drivers are often grossly idiotic and don't pay attention. Not how many grade crossing accidents you see on YouTube...
That said, it is indeed a major issue that the FRA rules apply to any rail line connected to the freight network that spans the nation. It would be far better if the regulations made clear exceptions for trains on passenger-only lines, hours of operation, etc.
For example, let's look at CalTrain. The main line up the peninsula only sees freight traffic at night. By setting operational rules that restrict speeds near freight trains, etc, this would allow much better equipment for CalTrain while continuing to let freight run at specific times.
The FRA very much needs to get with the program and allow better conditional standards.