There already is - the 97 AAR channels.
The issue that you have, is your location. The LIRR, MTA etc are all "captive" railroads. They do not interchange equipment or operations in the traditional sense - thus they can essentially do what they want as they do not have to worry about any other railroad (keeping it simple).
Freight on the other hand, can trade off engines to any other railroad and/or operate on trackage rights on another railroad. With the limited exception of cab signaled subdivisions, any railroads engine can lead another railroads train (i.e. UP engine as the leader on a CSX train).
The UP radio must be able to communicate on CSX channels, and all operate on the standard 97 channel plan. If CSX used PL tones, then CSX would need to swap in one of their radios (not going to happen) or place a CSX leader on (again, not going to happen unless cabs are needed) as it take time to re air test the train, arm/disarm EOT's or rearrange DPU consists.
So, using the AAR radio, you simply enter the radio channel used.
Aside from major railroad interchanges/cities, interference and overlap isn't as bad as railfans perceive it to be. You have 97 standard channels at 15k spacing to choose from.
With the exception of Riton and the GE branded radios, Neterma/JEM radios are all Kenwood or ICOM based mobile radios with the AAR interface. The Motorola radios were the same way.
Riton built theirs from the ground up (and I think they are the closest to Motorola quaility). I don't recall who OEM's GE branded radios.
Aside from that, commuter railroads, short lines and even some regionals can use whatever they want as their equipment isn't typically handed off to other railroads. I've seen CDM1250's used with the channels needed for their purposes.
All the major railroads use the clean cabs (reguardless of manufacturer) as all the cabling and power is a standard format and location. Basically plug and play in 2minutes.
NXDN was being pushed as the digital standard. However what was forgotten was that's backend equipment needed to be replaced, 10's of 1000's of locomotive radios, vehicle radios, handhelds, MOW equipment - how to digitally interface wayside equipment (and the list goes on) - which hasn't been figured out yet.
NS still runs a bunch of Motorola Railroad Astro Spectras and only being replaced as they fail beyond repair.
BNSF has been playing with NXDN in some of its yard, but generally (not always) confined to mechincal forces, and the like. It's kind of hard to switch or have a train work a yard when the incoming conductor doesn't have a NXDN radio.
Many of the early Nexterma radios and some JEMs are NXDN calible but not enabled (you can try to select a NXDN channel but will error out).
You also have to understand the 99% of railroad communications are simplex. In a metropolitan area, mountains or even on the open plains, a conductor walking a 8500+ft train isn't communicating well with the engineer. Often other trains ornthe dispatchers will have to relay information as the radio just doesn't reach. Although error correction is employed in All the digital formats, if the signal doesn't reach, it doesn't reach. Railroaders have very little toerlance for the digital sound as well as injected digital garbage that public safety is putting up with.
So far based on our testing, it's not going to be accepted by the rank and file as well as the safety committees for road operations.