I'm going to stick my neck out and say that CW 1 (as well as, maybe, CW2 & 3) will not be E, primarily because there are a ton of "outside agencies" which depend on having radio contact with the NYPD, such as State Parole, NYC Probation, NYC Sheriff, NYSP, various Federal agencies, and a few NGOs, etc.
The city is NOT going to give them encrypted radios, nor are they going to give them the key. And those citywide channels transmit "heavy" jobs on the initial calls and also when the jobs are in progress (if they're "heavy" enough).
Also, the reason why the NYPD is going full-speed on E goes back to the Summer of 2020 and the so-called "George Floyd riots." At that time, not only were the rioters monitoring the NYPD, they also had an abundance of CCRs and the like, transmitting false "13s" and "shots fired" in the middle of the window breaking, looting, and police car burning. That had to stop.
With that, I'll say that their main concern are those false radio runs being transmitted, and not what's heard over the radio. Also, their move to a Trunked system will give access to receiving with little chance (as discussed many times elsewhere) of anyone being able to program for transmitting (yeah, I know...everyone has some tech way of bypassing the key, etc., but that can be handled too), and may not go E, either. We'll see about that.
Re: Transit: the Port Authority Police use a trunked system on their PATH subway between NY and NJ, and, as far as I know, haven't experienced many, if any, problems. Granted, it's a smaller system, but it appears that being in a tunnel is not the main problem with Transit.