Lisa, below is what I remember about the Jr. story:

Gotti Jr as a strategy to try and out smart the feds he did a Proffer Session.

Proffer sessions are supposed to remain a secret however, the feds wanted to put jr. in the position, Penessi was in. (RUNNING SCARED)

The feds wanted the Gambino's to come after Gotti Jr so he would run to them for protection.

Before he proffered he sent his attorney (CARNISI) to go see Daniel Marino to tell him that this was his trial strategy. I believe he sent a message to Massino as well, not necessarily exactly what he was going to do meaning proffer, he asked if he could testify in his own defense?, If he did was he breaking any rules?, There clearly is a difference between testifying and proffering however, the proffer was supposed to be secret, so Jr, took a shot and the FEDS BURNED HIM.

The feds ended up trying 4 times to convict Gotti Jr. at trial. ( I NEVER SEEN THEM TRY ANYONE 4 times)

Nobody made a big deal about the proffer until Alite got a copy of it and he was show casing it calling Giotti Jr a RAT,

What I remember was Alite wanted to reconcile with Jr, and Jr. dismissed him calling him a DOG saying I chased you out of the neighborhood back in the day your a RAT, get out of here.

Alite then went on a campaign trying to convince everyone that Jr was a RAT.

I personally dont think Jr was a RAT, first of all NOT ONE PERSON GOT IN TROUBLE.
I think he broke Omerta by what he did however, just about every wiseguy breaks OMERTA, these days.

What most people dont know is that at one point back in the day
Jr actually out smarted the feds, they were building a case and sent out subpoena's to everyone in his crew, he had I think Agnello, seek out immunity to testify, the feds thought maybe he would flip or give them some evidence against Gotti Jr,
What happened was Agnello ended up confessing to the crime, he did not commit, and the feds never seen that coming, so now they couldn't charge Agnello, because they just gave him immunity from prosecution.

I remember seeing on you tube the video of Jr. up to see SR. at Marion, and in code telling Sr. what had happened and Sr. said I guess the guy that thought of that should get some stripes. (MEANING PROMOTED TO CAPO)

This is obviously what Pennesi was referring to and why he chose to stay away from Jr.