Which connection do you mean? There was a BMT-BRT connection on an el over Chestnut Street that connected the LIRR with what is now the J line. LIRR trains ran off the Atlantic branch, over Chestnut Street, and onto the Jamaica line. The LIRR then ran over the Broadway El, and terminated at the Chambers Street station. This happened in the 1900's and 1910's. I am not sure what kind of equipment the LIRR used for this service, but it ran a rapid transit like service on Atlantic Ave at the time, so it must have been whatever they used on the Atantic line.
The R44SI cars are not FRA compatible, they're FRA waivered. They had their window glazings replaced with FRA compatible lexan or something, and that's the extent of the modifications AFAIK. Structurally they're still R44s, same as the R44s on the A train, just in slightly better shape. SIRT does not interchange with freight railroads, yet remains under the control of the FRA for purely historical reasons. Given that, the FRA let NYC get away with relatively few changes to the cars in order to get them operating on the system.
By the same token, neither Baltimore's LRT cars, PATH's cars, nor NJT's Riverline cars are FRA compatible. They're all operated under a waiver from the FRA saying that in lieu of a beefed up body other precautions have been taken that satisfy the FRA's requirements, be they time-share of track, engineer training for the T/O, or other things.
And yes, Trucks and Cars do share the highway, I believe that was the point of ChuChuBob's statement. A sub-1000lb compact car can share the road with a 70,000lb truck, yet a 115,000lb LRV cannot share track with a 4000ton road freight. And keep in mind there's absolutely nothing to keep the truck and car separated except the presumed lane positions, which are purely up to the drivers to maintain. At least with a train there's the track to keep everything nice and ordered.